Contacts of the helix formed by residues 3 - 29 (chain w) in PDB entry 6AH0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 3 (chain w).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1w MET 3.2 6.3 + - - -
2w GLU* 1.3 68.4 - - - +
4w ILE* 1.3 67.0 + - - +
5w LEU 3.0 3.6 - - - +
6w GLU* 3.0 15.6 + - - -
7w GLN 3.6 5.2 + - - -
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Residues in contact with ILE 4 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2w GLU 3.2 8.1 + - - -
3w THR* 1.3 70.4 - - - +
5w LEU* 1.3 62.1 + - - +
7w GLN* 3.1 4.3 + - - +
8w GLN* 2.9 22.9 + - - -
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Residues in contact with LEU 5 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215u TYR* 6.1 1.2 - - - -
3w THR 3.0 2.0 + - - -
4w ILE* 1.3 75.8 - - - +
6w GLU* 1.3 56.2 + - - +
8w GLN* 3.9 0.6 - - - +
9w ARG* 2.9 26.2 + - - -
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Residues in contact with GLU 6 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3w THR 3.0 10.1 + - - -
5w LEU* 1.3 76.4 - - - +
7w GLN* 1.3 55.7 + - - +
9w ARG* 3.3 1.9 + - - +
10w ARG* 2.9 26.2 + - - -
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Residues in contact with GLN 7 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3w THR 3.6 5.5 + - - -
4w ILE* 3.1 7.6 + - - +
6w GLU* 1.3 72.7 - - - +
8w GLN* 1.3 59.1 + - - +
10w ARG* 3.2 3.4 + - - +
11w TYR* 2.9 25.5 + - - -
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Residues in contact with GLN 8 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4w ILE 2.9 17.3 + - - -
5w LEU* 4.0 0.9 - - - +
7w GLN* 1.3 71.4 - - - +
9w ARG* 1.3 61.3 + - - +
11w TYR* 3.2 2.9 + - - +
12w HIS* 2.9 20.8 + - - -
94w PHE* 6.2 4.9 - - - +
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Residues in contact with ARG 9 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214u GLN 6.0 3.1 - - - -
215u TYR* 6.6 0.4 - - - +
218u ILE* 6.6 0.4 - - - +
5w LEU 2.9 19.1 + - - -
6w GLU* 3.6 2.0 - - - +
8w GLN* 1.3 75.2 - - - +
10w ARG* 1.3 62.0 + - - +
11w TYR 3.0 0.5 + - - -
12w HIS* 3.1 3.7 + - - +
13w GLU* 2.9 20.1 + - - -
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Residues in contact with ARG 10 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6w GLU 2.9 17.4 + - - -
7w GLN* 3.2 3.8 + - - +
9w ARG* 1.3 71.1 - - - +
11w TYR* 1.3 55.5 + - - +
13w GLU* 3.4 2.2 + - - +
14w GLU* 2.9 25.5 + - - -
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Residues in contact with TYR 11 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7w GLN 2.9 14.3 + - - -
8w GLN* 3.6 4.5 - - - +
9w ARG 3.1 0.2 - - - -
10w ARG* 1.3 73.2 - - - +
12w HIS* 1.3 65.5 + - - +
14w GLU* 3.0 3.2 + - - +
15w LYS* 2.9 21.1 + - - -
90w GLN* 6.0 4.7 - - - +
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Residues in contact with HIS 12 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8w GLN 2.9 14.3 + - - -
9w ARG 3.7 2.5 - - - -
11w TYR* 1.3 73.3 - - - +
13w GLU* 1.3 56.2 + - - +
15w LYS* 3.5 2.4 + - - +
16w GLU* 3.0 24.9 + - - -
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Residues in contact with GLU 13 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9w ARG 2.9 13.7 + - - -
10w ARG* 3.7 3.8 - - - +
12w HIS* 1.3 73.8 - - - +
14w GLU* 1.3 58.7 + - - +
16w GLU* 3.2 3.4 + - - +
17w ARG* 2.9 23.7 + - - -
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Residues in contact with GLU 14 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10w ARG 2.9 15.5 + - - -
11w TYR* 3.0 3.1 + - - +
13w GLU* 1.3 71.7 - - - +
15w LYS* 1.3 67.1 + - - +
17w ARG* 2.9 12.3 + - - +
18w LEU* 2.9 12.1 + - - -
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Residues in contact with LYS 15 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11w TYR 2.9 13.4 + - - -
12w HIS* 3.8 3.8 - - - +
14w GLU* 1.3 75.8 - - - +
16w GLU* 1.3 62.2 + - - +
18w LEU* 3.2 1.5 + - - +
19w MET* 3.0 21.5 + - - -
87w ARG* 5.8 8.1 - - - +
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Residues in contact with GLU 16 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12w HIS 3.0 15.3 + - - -
13w GLU 3.2 4.9 + - - -
15w LYS* 1.3 74.5 - - - +
17w ARG* 1.3 56.8 + - - +
19w MET* 3.5 1.1 + - - +
20w ASP* 2.9 26.5 + - - -
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Residues in contact with ARG 17 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13w GLU 2.9 10.5 + - - -
14w GLU* 2.9 9.3 + - - +
16w GLU* 1.3 75.3 - - - +
18w LEU* 1.3 55.5 + - - +
20w ASP* 3.3 3.2 + - - +
21w VAL* 2.9 24.3 + - - -
139w TYR* 6.4 2.0 - - - +
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Residues in contact with LEU 18 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14w GLU 2.9 12.5 + - - -
15w LYS* 3.7 2.7 - - - +
17w ARG* 1.3 72.4 - - - +
19w MET* 1.3 67.0 + - - +
21w VAL* 2.9 12.0 + - - +
22w MET* 2.9 13.3 + - - -
83w GLU 6.6 0.2 - - - -
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Residues in contact with MET 19 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243u VAL* 4.8 9.8 - - - +
15w LYS 3.0 14.0 + - - -
16w GLU* 3.8 2.9 - - - +
18w LEU* 1.3 73.2 - - - +
20w ASP* 1.3 57.4 + - - +
22w MET* 3.5 1.0 + - - +
23w ALA* 2.9 26.9 + - - -
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Residues in contact with ASP 20 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16w GLU 2.9 15.3 + - - -
17w ARG* 3.6 4.5 - - - +
19w MET* 1.3 75.1 - - - +
21w VAL* 1.3 58.1 + - - +
23w ALA* 3.8 1.0 - - - +
24w LYS* 2.9 24.9 + - - -
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Residues in contact with VAL 21 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17w ARG 2.9 10.3 + - - -
18w LEU* 2.9 9.7 + - - +
20w ASP* 1.3 71.9 - - - +
22w MET* 1.3 58.6 + - - +
23w ALA 3.0 1.3 - - - -
24w LYS* 3.0 4.4 + - - +
25w GLU* 2.9 24.6 + - - -
142w LEU 4.5 15.7 - - - -
143w HIS* 6.1 0.9 - - - +
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Residues in contact with MET 22 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243u VAL* 5.6 2.5 - - - -
18w LEU 2.9 12.9 + - - -
19w MET* 3.9 1.1 - - - +
21w VAL* 1.3 73.8 - - - +
23w ALA* 1.3 56.6 + - - +
25w GLU* 3.8 3.0 - - - +
26w MET* 2.9 22.9 + - - -
80w GLU* 6.0 5.4 - - - +
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Residues in contact with ALA 23 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243u VAL* 3.8 25.6 - - - +
247u VAL* 4.4 12.9 - - - +
19w MET 2.9 18.6 + - - -
20w ASP* 3.8 1.8 - - - +
22w MET* 1.3 76.2 - - - +
24w LYS* 1.3 63.3 + - - +
25w GLU 3.2 0.2 - - - -
26w MET* 3.4 2.6 + - - +
27w LEU* 2.9 19.6 + - - -
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Residues in contact with LYS 24 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20w ASP 2.9 16.3 + - - -
21w VAL* 3.0 3.6 + - - +
23w ALA* 1.3 73.9 - - - +
25w GLU* 1.3 62.3 + - - +
27w LEU* 2.9 11.0 + - - +
28w THR* 2.9 13.0 + - - -
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Residues in contact with GLU 25 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21w VAL 2.9 13.3 + - - -
22w MET* 3.9 4.0 - - - +
24w LYS* 1.3 70.1 - - - +
26w MET* 1.3 64.3 + - - +
27w LEU 2.8 5.1 + - - -
28w THR* 3.0 11.9 + - - +
29w LYS* 3.2 12.0 + - - +
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Residues in contact with MET 26 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243u VAL 6.1 0.4 - - - -
244u CYS* 6.3 3.4 - - - +
247u VAL* 5.9 1.1 - - - -
22w MET 2.9 16.1 + - - -
23w ALA* 3.4 5.8 + - - +
25w GLU* 1.3 73.1 - - - +
27w LEU* 1.3 59.3 + - - +
29w LYS 4.3 6.1 - - - -
30w LYS* 3.3 24.1 - - - +
32w THR* 5.8 1.6 - - - +
33w LEU* 5.4 8.1 - - - +
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Residues in contact with LEU 27 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247u VAL* 5.2 9.4 - - - +
23w ALA 2.9 13.4 + - - -
24w LYS* 2.9 5.4 + - - +
25w GLU 2.8 3.6 + - - -
26w MET* 1.3 77.0 - - - +
28w THR* 1.3 64.4 + - - +
29w LYS 3.3 0.3 + - - -
30w LYS 4.2 3.5 + - - -
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Residues in contact with THR 28 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24w LYS 2.9 13.1 + - - -
25w GLU* 3.0 2.4 + - - +
27w LEU* 1.3 75.7 - - - +
29w LYS* 1.3 57.4 + - - +
30w LYS 4.3 0.2 + - - -
65w ASP* 4.8 13.9 - - - -
66w GLY 5.0 4.7 + - - +
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Residues in contact with LYS 29 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25w GLU 3.2 10.7 + - - +
26w MET* 3.7 6.3 - - - +
28w THR* 1.3 79.1 - - - +
30w LYS* 1.3 57.2 + - - +
31w SER 2.9 12.9 + - - -
32w THR* 2.9 15.6 + - - -
65w ASP 6.5 0.2 - - - -
66w GLY 5.3 6.1 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il