Contacts of the helix formed by residues 9 - 26 (chain w) in PDB entry 3J9X
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 SER 9 (chain w).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S THR* 5.5 13.3 - - - +
51S LYS* 6.0 4.9 - - - -
8w ARG* 1.3 74.9 - - - +
10w TYR* 1.3 60.4 + - - +
11w SER* 3.6 9.7 + - - -
12w GLN* 2.8 35.7 + - - +
13w ARG* 2.8 27.0 + - - +
53x THR* 4.3 3.6 - - - -
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Residues in contact with TYR 10 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S PRO* 4.9 12.1 - - + -
10T TYR* 2.8 44.9 + + - -
11T SER* 5.5 0.2 - - - -
9w SER* 1.3 73.5 - - - +
11w SER* 1.3 71.4 - - - +
13w ARG* 3.0 5.0 + - + -
14w TYR* 2.9 46.8 + + + +
45x PHE* 4.1 1.1 - + - -
46x GLN* 3.3 35.7 + - - +
49x VAL* 3.8 15.3 - - + -
50x PRO* 3.5 38.6 - - + -
53x THR* 3.5 32.7 - - + +
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Residues in contact with SER 11 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S GLN* 5.1 9.0 - - - -
46S GLN* 2.8 50.3 + - - +
47S THR* 4.8 4.3 - - - -
50S PRO* 4.8 0.7 - - - +
10T TYR* 5.0 1.7 + - - -
9w SER* 3.2 10.0 + - - -
10w TYR* 1.3 87.5 - - - +
12w GLN* 1.3 60.6 + - - +
14w TYR* 4.0 3.0 - - - +
15w ALA* 3.0 30.2 + - - +
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Residues in contact with GLN 12 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567 T 4.5 3.0 + - - -
43S GLN* 6.1 2.5 - - - +
40v VAL* 5.2 1.7 - - - +
43v GLN* 5.3 8.6 - - + +
44v ASN* 2.9 34.3 + - - +
47v THR* 4.6 18.8 + - - +
48v ASN* 5.2 1.6 - - - +
7w SER 4.2 5.1 + - - +
8w ARG* 3.6 29.7 - - - +
9w SER* 2.8 40.2 + - - +
11w SER* 1.3 78.6 - - - +
13w ARG* 1.3 66.0 + - - +
15w ALA* 3.7 4.8 - - - +
16w LYS* 3.2 24.4 + - - +
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Residues in contact with ARG 13 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557 A 3.4 54.1 + - + +
567 T 3.6 40.4 + - - -
2948 T 4.1 7.7 + - - -
2958 A 5.3 5.3 + - - -
8w ARG* 4.1 6.5 - - + +
9w SER 2.8 22.3 + - - +
10w TYR* 3.0 10.5 + - + +
12w GLN* 1.3 72.6 - - - +
14w TYR* 1.3 62.6 + - - +
17w TRP* 3.1 23.9 + - - +
45x PHE* 4.6 7.6 - - + -
49x VAL* 3.7 21.2 + - - +
52x PHE* 4.6 4.8 - - - +
53x THR* 2.8 43.8 + - - +
56x ASN* 4.3 10.7 - - - +
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Residues in contact with TYR 14 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S GLN* 6.2 1.8 - - - -
10T TYR* 5.5 1.3 - - - -
10w TYR* 2.9 36.3 + + + +
11w SER* 4.1 3.4 - - - +
13w ARG* 1.3 77.2 - - - +
15w ALA* 1.3 69.8 + - - +
17w TRP* 3.1 17.0 + + - +
18w GLN* 2.7 57.1 + - + +
42x GLN* 3.7 8.9 + - - +
45x PHE* 3.4 35.9 - + + -
46x GLN* 2.9 36.4 + - + -
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Residues in contact with ALA 15 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40v VAL* 4.0 20.5 - - + +
11w SER 3.0 18.8 + - - +
12w GLN* 3.4 8.3 + - - +
14w TYR* 1.3 83.6 - - - +
16w LYS* 1.3 62.8 + - - +
18w GLN* 3.3 6.1 + - - +
19w ALA* 3.2 19.6 + - - +
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Residues in contact with LYS 16 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557 A 3.3 42.0 + - - +
567 T 4.3 13.8 + - - +
2858 A 3.8 38.2 + - - +
2868 T 2.8 35.4 + - - +
37v VAL* 4.9 7.9 - - + -
40v VAL* 3.9 19.5 - - + +
44v ASN* 5.0 2.5 - - - +
8w ARG* 6.0 0.2 - - - +
12w GLN 3.2 13.0 + - - +
15w ALA* 1.3 77.2 - - - +
17w TRP* 1.3 67.1 + - - +
19w ALA* 3.1 4.5 + - - +
20w LYS* 3.0 25.4 + - + +
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Residues in contact with TRP 17 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 A 5.3 0.4 - - - -
547 T 3.6 19.0 + - + +
557 A 3.5 28.8 - - - +
2958 A 5.0 0.2 - + - -
2968 T 2.9 37.8 + - + -
2978 A 5.4 0.2 - - - -
13w ARG 3.1 18.5 + - - +
14w TYR* 3.1 21.9 + + - +
16w LYS* 1.3 77.4 - - - +
18w GLN* 1.3 94.7 + - - +
20w LYS* 3.4 2.0 + - - +
21w PHE* 2.9 52.1 + + + +
41x ALA* 4.1 21.1 - - + -
42x GLN* 4.3 5.6 - - + -
45x PHE* 3.5 45.2 - + + -
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Residues in contact with GLN 18 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14w TYR* 2.7 53.4 + - + +
15w ALA* 3.5 7.0 - - - +
17w TRP* 1.3 86.9 - - - +
19w ALA* 1.3 63.1 + - - +
21w PHE* 3.2 6.7 + - - -
22w ASN* 2.9 63.0 + - - +
42x GLN* 3.2 36.4 - - - +
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Residues in contact with ALA 19 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36v ASN* 3.4 33.6 - - - +
37v VAL* 3.7 16.8 - - + -
40v VAL* 4.3 6.7 - - + -
15w ALA 3.2 9.2 + - - +
16w LYS* 3.1 9.9 + - - +
18w GLN* 1.3 80.5 - - - +
20w LYS* 1.3 58.6 + - - +
22w ASN* 3.5 8.8 + - - +
23w ALA* 3.1 27.0 + - - +
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Residues in contact with LYS 20 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547 T 3.5 40.4 + - + +
557 A 3.1 29.8 + - - +
2868 T 2.8 31.6 + - - +
2878 A 3.2 27.6 + - - -
33v ILE* 4.0 22.0 - - + -
37v VAL* 3.7 15.5 - - + -
16w LYS* 3.0 20.5 + - + +
17w TRP 3.9 2.7 - - - +
19w ALA* 1.3 74.1 - - - +
21w PHE* 1.3 67.0 + - - +
23w ALA* 3.3 3.5 + - - +
24w PHE* 3.0 24.4 + - - +
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Residues in contact with PHE 21 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 A 6.1 3.8 - + - -
547 T 5.6 2.4 - - - +
2968 T 5.8 0.2 - - - -
2978 A 4.5 24.0 - - - -
17w TRP* 2.9 46.8 + + + +
18w GLN* 3.6 11.4 - - - +
20w LYS* 1.3 76.7 - - - +
22w ASN* 1.3 73.2 + - - +
24w PHE* 3.3 12.4 + + - +
25w SER* 3.1 23.5 + - - -
34x LEU* 4.1 30.1 - - + -
37x VAL* 4.6 4.7 - - + -
38x SER* 3.6 36.6 - - - -
41x ALA* 4.3 11.9 - - + -
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Residues in contact with ASN 22 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36v ASN* 4.0 11.7 - - - +
18w GLN* 2.9 52.7 + - - +
19w ALA* 3.6 7.7 - - - +
21w PHE* 1.3 81.1 - - - +
23w ALA* 1.3 63.2 + - - +
25w SER* 2.6 25.7 + - - -
26w ASN* 3.6 3.6 + - - +
38x SER* 5.5 2.4 + - - -
42x GLN* 4.7 3.1 + - - -
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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
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32v THR* 3.6 14.3 - - + +
33v ILE* 3.8 28.5 - - + -
36v ASN* 3.4 17.7 - - - +
19w ALA 3.1 12.2 + - - +
20w LYS* 3.5 10.5 - - + +
21w PHE 3.2 0.2 - - - -
22w ASN* 1.3 78.7 - - - +
24w PHE* 1.3 64.4 + - - +
26w ASN* 3.1 21.8 + - - +
29w VAL* 3.5 9.5 - - - +
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Residues in contact with PHE 24 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 A 3.7 52.0 - - + -
547 T 4.6 8.1 - - - +
20w LYS 3.0 16.5 + - - +
21w PHE* 3.3 11.4 + + - +
23w ALA* 1.3 76.7 - - - +
25w SER* 1.3 62.2 + - - +
26w ASN 3.0 1.4 + - - -
29w VAL* 4.0 5.6 - - - +
30w ALA* 3.3 45.3 + - + +
33w ILE* 4.3 14.4 - - + -
34w LEU* 4.0 22.4 - - + -
24x PHE* 4.4 9.2 - + - -
34x LEU* 3.5 30.7 - - + -
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Residues in contact with SER 25 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21w PHE* 3.1 15.2 + - - -
22w ASN* 2.6 23.8 + - - -
24w PHE* 1.3 76.4 - - - +
26w ASN* 1.3 63.3 + - - +
27w PRO* 3.2 4.5 - - - +
30w ALA* 5.0 0.4 - - - +
31x SER* 3.5 21.7 - - - +
34x LEU* 3.9 35.2 - - - -
35x SER* 4.6 6.4 - - - -
38x SER* 4.6 8.5 + - - -
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Residues in contact with ASN 26 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28v THR* 4.9 3.0 - - - +
32v THR* 4.0 19.8 + - + +
22w ASN 3.6 2.2 + - - +
23w ALA 3.1 14.7 + - - +
24w PHE 3.0 1.8 + - - +
25w SER* 1.3 78.6 + - - +
27w PRO* 1.4 68.2 - - - +
28w THR* 2.7 32.5 + - - +
29w VAL* 2.7 35.5 + - + -
30w ALA* 2.9 11.5 + - - -
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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) + - + + + + + -
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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