Contacts of the helix formed by residues 4 - 22 (chain A) in PDB entry 5U8T
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 ASP 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 2.6 34.5 + - - +
2A TYR 2.6 18.8 + - - +
3A GLY* 1.3 71.0 - - - +
5A LEU* 1.3 64.3 + - - +
6A GLY 3.1 2.9 - - - -
7A ASN* 2.6 47.7 + - + +
8A LYS* 3.7 4.7 + - - +
43A GLU* 5.3 0.3 - - - +
49C TRP* 5.5 0.2 - - - -
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Residues in contact with LEU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A TYR 5.4 0.9 - - - +
3A GLY 3.3 1.9 - - - -
4A ASP* 1.3 87.2 + - - +
6A GLY* 1.3 60.6 + - - +
7A ASN 3.3 0.7 + - - -
8A LYS* 3.5 27.0 + - + +
9A LEU* 3.9 4.2 + - - +
36A ILE* 3.6 28.6 - - + +
39A ASN* 3.8 31.0 - - + +
40A ILE* 4.0 23.8 - - + +
43A GLU* 5.2 11.0 - - - +
82A ASN* 6.2 0.4 - - - +
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Residues in contact with GLY 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLY 3.8 6.0 + - - -
4A ASP 3.1 0.8 - - - -
5A LEU* 1.3 78.6 - - - +
7A ASN* 1.3 59.7 + - - +
9A LEU* 3.0 10.5 + - - +
10A VAL* 2.9 29.5 + - - +
40A ILE* 4.2 19.0 - - - +
82A ASN* 5.2 5.3 - - - +
85A CYS* 4.3 20.5 - - - +
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Residues in contact with ASN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLY 3.4 10.4 + - - +
4A ASP* 2.6 39.7 + - - +
6A GLY* 1.3 71.2 - - - +
8A LYS* 1.3 59.2 + - + +
10A VAL* 3.2 12.3 - - + +
11A LEU* 2.9 31.6 + - - +
81A ARG* 3.4 28.1 + - - +
85A CYS* 4.3 5.0 - - - -
9C VAL* 4.7 0.4 - - - +
10C LEU* 5.7 6.0 - - + +
13C GLY* 5.1 8.8 - - - -
49C TRP* 5.5 1.8 - - - +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ASP 4.5 5.4 - - - +
5A LEU* 3.6 24.9 - - + +
7A ASN* 1.3 76.2 - - + +
9A LEU* 1.3 58.4 + - - +
11A LEU* 3.3 21.8 - - + +
12A GLU* 2.9 27.9 + - - +
36A ILE* 5.7 4.9 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU 3.9 2.4 + - - +
6A GLY* 3.0 16.5 + - - +
8A LYS* 1.3 77.9 - - - +
10A VAL* 1.3 63.4 + - - +
12A GLU* 3.2 12.4 + - + +
13A ALA* 2.9 23.9 + - - +
33A HIS* 5.1 6.5 - - + +
36A ILE* 4.1 20.4 - - + -
37A ILE* 3.5 32.5 - - + -
40A ILE* 4.3 9.4 - - + -
85A CYS* 3.9 16.4 - - + +
86A LEU* 4.9 2.7 - - + +
89A TYR* 3.4 47.6 - - + -
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY 2.9 10.2 + - - +
7A ASN* 3.2 33.4 - - + +
9A LEU* 1.3 78.7 - - + +
11A LEU* 1.3 59.9 + - - +
13A ALA* 3.1 8.2 + - + +
14A LYS* 2.9 25.3 + - - +
85A CYS* 5.2 7.4 - - + +
88A ALA* 6.2 1.3 - - + -
89A TYR* 6.0 0.2 - - - -
6C ILE* 3.5 33.6 - - + +
9C VAL* 3.5 31.6 - - + -
10C LEU* 5.0 14.0 - - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN 2.9 18.6 + - - +
8A LYS* 3.3 25.4 - - + +
10A VAL* 1.3 75.9 - - - +
12A GLU* 1.3 60.9 + - - +
14A LYS* 2.8 32.2 + - + +
15A ARG* 3.1 12.0 + - - +
10C LEU* 4.5 26.9 - - + -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS 2.9 14.2 + - - +
9A LEU* 3.3 11.0 - - - +
11A LEU* 1.3 75.7 - - - +
13A ALA* 1.3 58.7 + - - +
15A ARG* 3.1 23.6 - - - +
16A THR* 2.9 34.0 + - - +
30A PRO* 3.8 25.3 - - - +
31A MET 5.5 0.2 - - - +
33A HIS* 3.5 36.7 - - + +
89A TYR* 3.9 16.5 - - - -
93A ARG* 5.1 1.7 + - - -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 2.9 12.8 + - - +
10A VAL* 3.1 18.8 - - - +
11A LEU 3.0 0.2 - - - -
12A GLU* 1.3 77.7 - - - +
14A LYS* 1.3 57.8 + - - +
16A THR* 3.1 10.9 - - - +
17A LYS* 2.9 34.1 + - - +
89A TYR* 4.5 15.7 - - + -
92A LEU* 3.5 16.8 - - + -
6C ILE* 3.7 12.3 - - + -
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL 2.9 7.9 + - - +
11A LEU* 2.8 22.4 + - + +
13A ALA* 1.3 74.3 - - - +
15A ARG* 1.3 67.3 + - - +
17A LYS* 3.0 6.0 + - - +
18A GLN* 3.0 38.1 + - + +
6C ILE* 3.5 26.2 - - + +
7C ASP* 4.6 6.7 + - - -
10C LEU* 4.4 15.9 - - + -
103C HIS* 5.4 2.5 - - - -
171C GLU* 2.6 49.9 + - - +
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3585 LEU* 6.4 0.6 - - - +
6685 LEU* 4.8 17.0 + - - +
6705 PRO* 3.8 29.9 - - - +
11A LEU 3.1 6.8 + - - +
12A GLU* 3.1 34.1 - - - +
14A LYS* 1.3 80.5 - - - +
16A THR* 1.3 62.2 + - - +
18A GLN* 3.0 14.0 + - - +
19A LEU* 2.9 42.4 + - + +
30A PRO* 6.2 1.1 - - - -
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Residues in contact with THR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 2.9 32.9 + - - +
13A ALA* 3.1 21.8 - - - +
15A ARG* 1.3 76.6 - - - +
17A LYS* 1.3 65.0 + - - +
19A LEU* 3.5 19.5 + - - +
20A TYR* 3.6 10.4 + - - +
29A LEU* 4.6 10.9 - - - +
30A PRO* 3.8 20.1 - - - +
89A TYR* 5.8 2.9 - - + -
92A LEU* 3.5 17.0 - - + +
93A ARG* 6.0 3.5 + - - +
96A ILE* 5.9 1.7 - - - +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 2.9 21.7 + - - +
14A LYS* 3.2 7.4 - - + +
16A THR* 1.3 78.0 - - - +
18A GLN* 1.3 60.0 + - - +
20A TYR* 3.2 8.4 + - - +
21A ALA* 2.8 29.5 + - - +
92A LEU* 3.5 27.4 - - + -
5C ASP* 2.8 29.3 + - - +
6C ILE* 3.2 36.6 - - + +
7C ASP* 4.8 2.8 + - - -
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 3.0 36.8 + - + +
15A ARG* 3.0 13.7 + - - +
17A LYS* 1.3 82.0 - - - +
19A LEU* 1.3 59.9 + - + +
21A ALA* 3.3 25.3 + - - +
22A ARG* 4.2 1.6 + - - +
23A SER* 3.6 12.1 - - - +
171C GLU* 5.2 4.5 + - - +
174C LYS* 5.9 4.4 - - - +
178C LYS* 5.5 10.9 - - - +
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3545 GLU* 5.6 4.3 - - - +
3585 LEU* 4.4 22.2 - - + -
3625 ARG* 6.1 1.1 - - - +
15A ARG* 2.9 28.2 + - + +
16A THR* 3.8 23.6 - - - +
17A LYS 3.2 0.6 - - - -
18A GLN* 1.3 76.7 - - - +
20A TYR* 1.3 55.8 + - - +
23A SER* 2.9 18.6 + - - +
24A ASN 4.3 2.4 - - - +
26A ASP 5.2 0.3 + - - -
27A VAL* 4.7 18.1 + - - +
28A ASN 5.5 4.5 - - - +
30A PRO* 4.3 22.2 - - + -
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR 3.6 7.6 + - - +
17A LYS* 3.2 8.2 + - - +
18A GLN 3.2 0.2 - - - -
19A LEU* 1.3 77.6 - - - +
21A ALA* 1.3 62.7 + - - +
22A ARG 4.3 0.2 - - - -
23A SER* 3.1 18.9 + - - -
25A GLN* 4.2 31.2 - - + +
27A VAL* 5.3 10.8 - - + +
96A ILE* 3.4 35.7 - - + -
99A SER* 4.6 13.8 + - - -
103A ASN* 6.3 0.7 - - - -
5B ALA* 3.3 30.2 - - + +
6B HIS* 5.9 2.5 - + - -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 2.8 21.9 + - + +
18A GLN* 3.3 26.6 + - - +
20A TYR* 1.3 73.8 - - - +
22A ARG* 1.3 64.2 + - - +
6B HIS* 4.9 9.7 + - - -
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Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3495 PHE* 5.2 9.7 - - - +
3505 THR* 5.3 2.2 - - - +
3515 GLU* 3.1 59.2 + - - +
18A GLN 4.2 2.5 + - - +
20A TYR 4.3 0.7 - - - -
21A ALA* 1.3 77.4 - - - +
23A SER* 1.3 60.9 + - - +
24A ASN* 3.7 14.3 - - - +
25A GLN* 4.8 1.3 + - - +
6B HIS* 5.6 4.9 + - - -
178C LYS* 6.1 6.7 - - + +
182C GLU* 5.3 12.9 + - - +
185C LYS* 3.6 25.0 - - - +
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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