Contacts of the helix formed by residues 3 - 23 (chain B) in PDB entry 5WC9
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 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASP* 1.3 80.3 + - - +
4B PRO* 1.3 75.1 - - - +
5B GLU* 3.0 23.0 + - - -
6B ILE* 3.0 37.7 + - - +
7B ARG* 3.1 20.6 + - - +
57B PHE* 5.3 0.2 - - - -
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Residues in contact with PRO 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 1.3 88.1 - - - +
5B GLU* 1.3 71.7 + - + +
7B ARG* 3.8 32.1 + - - +
8B GLU* 3.3 22.3 + - - +
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Residues in contact with GLU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 3.0 25.9 + - - -
4B PRO* 1.3 88.1 - - + +
6B ILE* 1.3 59.2 + - - +
8B GLU* 3.5 5.3 + - - +
9B LEU* 2.9 31.6 + - + +
57B PHE* 3.7 31.0 - - + -
61B CYS* 5.8 1.1 - - - -
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASP* 4.6 14.1 - - - +
3B SER* 3.0 31.4 + - - +
5B GLU* 1.3 74.2 - - - +
7B ARG* 1.3 60.9 + - + +
9B LEU* 3.0 8.0 + - - +
10B GLU* 2.8 45.6 + - + +
57B PHE* 4.4 15.0 - - + -
149B VAL* 3.9 36.6 - - + +
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Residues in contact with ARG 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASP* 2.8 33.0 + - - +
3B SER* 3.1 12.5 + - - +
4B PRO* 4.0 38.2 - - + +
6B ILE* 1.3 76.8 - - + +
8B GLU* 1.3 58.0 + - - +
10B GLU* 3.3 13.4 + - - +
11B LYS* 3.0 29.2 + - - +
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO 3.3 17.0 + - - +
5B GLU* 3.9 5.6 - - - +
7B ARG* 1.3 77.1 - - - +
9B LEU* 1.3 60.8 + - - +
11B LYS* 4.0 9.3 - - - +
12B PHE* 3.3 22.2 + - - +
64B LYS* 4.7 9.9 - - - -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU 2.9 14.7 + - - +
6B ILE* 3.0 8.0 + - - +
8B GLU* 1.3 76.5 - - - +
10B GLU* 1.3 63.8 + - - +
12B PHE* 3.5 3.8 + - - +
13B ALA* 3.0 24.1 + - - +
50B PHE* 5.4 4.1 - - + -
53B LEU* 4.4 13.7 - - + +
57B PHE* 3.9 28.9 - - + -
60B ALA* 3.6 31.9 - - + +
61B CYS* 4.6 9.9 - - - -
64B LYS* 3.6 38.1 - - + +
149B VAL* 4.3 14.1 - - + -
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASP* 5.8 0.2 - - - +
6B ILE* 2.8 37.5 + - + +
7B ARG* 3.7 12.3 - - - +
9B LEU* 1.3 70.8 - - - +
11B LYS* 1.3 66.1 + - - +
13B ALA* 3.2 3.6 + - - +
14B ASN* 2.9 38.8 + - - +
53B LEU* 3.8 22.2 - - + +
149B VAL 6.0 0.7 - - - -
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Residues in contact with LYS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG 3.0 17.0 + - - +
8B GLU* 4.0 9.0 - - - +
9B LEU 3.3 0.2 - - - -
10B GLU* 1.3 78.0 - - - +
12B PHE* 1.3 58.0 + - - +
14B ASN* 3.4 7.3 + - - +
15B GLU* 2.8 73.9 + - + +
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU 3.3 16.6 + - - +
9B LEU 3.9 2.9 - - - +
10B GLU 3.3 0.6 - - - -
11B LYS* 1.3 79.2 - - - +
13B ALA* 1.3 51.1 + - - +
15B GLU* 3.8 13.1 - - + +
16B PHE* 2.6 49.9 + + + +
50B PHE* 3.7 31.6 - + - -
64B LYS* 3.6 36.3 - - + -
67B LEU* 4.1 8.7 - - + -
68B SER* 3.6 41.7 - - - -
71B LEU* 4.8 12.8 - - + -
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 3.0 19.0 + - - +
10B GLU* 3.2 6.5 + - - +
12B PHE* 1.3 76.1 - - - +
14B ASN* 1.3 65.7 + - - +
16B PHE* 3.5 2.6 + - - +
17B LYS* 3.2 22.3 + - - +
50B PHE* 3.9 30.1 - - + +
51B GLU* 3.8 27.4 - - - +
53B LEU* 4.5 8.1 - - + -
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 2.9 27.9 + - - +
11B LYS* 3.8 6.2 - - - +
13B ALA* 1.3 79.5 - - - +
15B GLU* 1.3 65.4 + - + +
17B LYS* 3.2 13.3 + - - +
18B VAL* 3.2 19.9 + - - +
51B GLU 4.9 4.0 - - - +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 2.8 54.9 + - + +
12B PHE* 3.8 11.7 - - + +
14B ASN* 1.3 77.2 - - + +
16B PHE* 1.3 63.3 + - - +
18B VAL* 3.2 11.0 - - + +
19B ARG* 3.1 38.8 + - - +
71B LEU* 5.3 0.9 - - - -
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 2.6 37.5 + + + +
13B ALA* 3.8 4.7 - - - +
15B GLU* 1.3 74.7 - - - +
17B LYS* 1.3 56.5 + - - +
19B ARG 4.0 0.2 - - - -
20B ARG* 3.0 36.7 + - + +
30B VAL* 4.2 20.0 - - + -
47B ILE* 4.3 9.4 - - + -
50B PHE* 4.5 10.3 - + - -
51B GLU* 3.8 33.0 - - + -
67B LEU* 3.7 40.2 - - + -
70B TRP* 3.9 23.8 - + - -
71B LEU* 4.0 27.4 - - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 3.2 14.5 + - - +
14B ASN* 3.6 10.5 - - - +
15B GLU 3.2 0.6 - - - -
16B PHE* 1.3 74.3 - - - +
18B VAL* 1.3 69.2 + - + +
20B ARG* 3.3 4.6 + - - +
21B ILE* 3.0 45.9 + - + +
51B GLU* 4.1 36.1 - - + +
180C A 5.9 3.4 - - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN 3.2 12.3 - - - +
15B GLU* 3.2 26.0 - - + +
17B LYS* 1.3 79.2 - - + +
19B ARG* 1.3 62.2 + - + +
21B ILE* 3.1 8.8 + - + +
22B LYS* 2.8 31.2 + - - +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 3.1 27.3 + - - +
16B PHE 4.4 0.2 - - - +
18B VAL* 1.3 80.8 - - + +
20B ARG* 1.3 62.4 + - - +
22B LYS* 4.0 24.3 - - - +
23B LEU* 3.1 31.7 + - - +
71B LEU* 3.9 36.3 + - + +
72B GLU* 5.0 2.8 - - - +
75B GLU* 2.1 42.7 + - - +
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.0 32.6 + - + +
17B LYS* 3.6 6.3 - - - +
19B ARG* 1.3 77.8 - - - +
21B ILE* 1.3 87.4 + - - +
23B LEU* 3.4 7.1 + - - +
24B GLY 3.1 3.8 + - - -
25B TYR* 3.0 50.6 + - + +
26B THR 4.4 2.5 - - - -
27B GLN* 3.4 16.5 - - - +
30B VAL* 3.6 31.9 - - + -
51B GLU* 2.0 52.4 + - - -
70B TRP* 5.5 2.2 - - + -
71B LEU* 4.8 3.7 - - - +
179C C 2.7 33.4 + - - -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 3.0 35.4 + - + +
18B VAL* 3.7 6.5 - - + +
20B ARG* 1.3 99.3 - - - +
22B LYS* 1.3 60.7 + - - +
24B GLY* 2.9 20.3 + - - +
25B TYR 4.6 4.3 - - - +
179C C 5.3 0.7 - - - +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL 2.8 15.2 + - - +
19B ARG* 4.0 32.8 + - - +
21B ILE* 1.3 78.0 - - - +
23B LEU* 1.3 66.0 + - + +
24B GLY 3.6 0.3 + - - -
75B GLU* 4.8 10.9 + - - -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 3.1 22.3 + - + +
20B ARG* 3.7 2.5 - - - +
21B ILE 3.1 0.8 - - - -
22B LYS* 1.3 85.3 - - + +
24B GLY* 1.3 62.8 + - - +
25B TYR* 3.4 28.0 + - + -
70B TRP* 5.8 0.7 - - + -
71B LEU* 4.1 16.2 - - + -
74B ALA* 3.3 29.4 - - + +
75B GLU* 4.0 30.3 - - - +
76B GLN 5.1 5.2 - - - +
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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