Contacts of the helix formed by residues 2 - 16 (chain B) in PDB entry 3ECS
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 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MSE 1.3 83.4 - - - +
3B ASP* 1.3 60.0 + - - +
4B LYS* 3.0 22.0 + - - +
5B GLU* 2.9 29.4 + - - +
6B LEU* 2.5 38.7 + - - +
33B PHE* 5.3 1.9 - - - -
53B ILE* 6.1 2.2 - - - -
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Residues in contact with ASP 3 (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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2B ASP* 1.3 77.4 + - - +
4B LYS* 1.3 61.7 + - + +
6B LEU* 3.0 5.1 + - - +
7B ILE* 2.8 40.0 + - + +
53B ILE* 4.0 11.5 - - - +
56B LEU* 3.0 45.7 - - + +
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Residues in contact with LYS 4 (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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2B ASP* 3.0 12.4 + - - +
3B ASP* 1.3 81.1 - - + +
5B GLU* 1.3 57.5 + - + +
7B ILE* 3.9 13.6 - - + +
8B GLU* 2.9 34.7 + - - +
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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
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1B MSE 3.1 25.7 - - + +
2B ASP* 2.9 35.6 + - + +
4B LYS* 1.3 77.3 - - + +
6B LEU* 1.3 62.0 + - - +
7B ILE 3.2 0.2 - - - -
8B GLU* 3.1 18.6 - - - +
9B TYR* 3.0 24.9 + - - +
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Residues in contact with LEU 6 (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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1B MSE 3.6 14.6 - - + +
2B ASP 2.5 21.9 + - - +
3B ASP 3.3 3.1 - - - +
5B GLU* 1.3 71.9 - - - +
7B ILE* 1.3 63.6 + - + +
9B TYR* 3.5 3.1 + - - +
10B PHE* 3.1 23.9 + - - +
29B THR* 4.0 30.9 - - - +
30B LEU* 5.1 0.4 - - + -
33B PHE* 4.2 12.1 - - + -
53B ILE* 3.4 55.9 - - + +
56B LEU* 3.8 20.0 - - + -
57B CYS* 4.4 12.8 - - - -
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Residues in contact with ILE 7 (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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3B ASP* 2.8 28.3 + - + +
4B LYS* 3.9 13.0 - - + +
6B LEU* 1.3 79.5 - - + +
8B GLU* 1.3 58.4 + - + +
10B PHE* 4.0 9.0 - - + +
11B LYS* 3.3 35.5 + - + +
56B LEU* 4.8 28.7 - - + +
57B CYS* 5.9 3.1 - - - -
59B VAL* 6.5 0.2 - - + -
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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 LYS* 2.9 17.6 + - - +
5B GLU* 3.1 33.8 + - - +
6B LEU 3.1 0.6 - - - -
7B ILE* 1.3 74.8 - - + +
9B TYR* 1.3 69.5 + - - +
10B PHE 2.9 1.3 - - - -
11B LYS* 2.7 18.2 + - - +
12B SER* 2.9 14.7 + - - -
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Residues in contact with TYR 9 (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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1B MSE 3.9 9.2 - - + -
5B GLU 3.0 11.8 + - - +
6B LEU* 3.8 4.5 - - - +
8B GLU* 1.3 79.2 - - - +
10B PHE* 1.3 56.4 + - - +
12B SER* 3.1 9.3 + - - -
13B GLN* 2.9 69.7 + - + +
28B ARG* 4.3 5.8 + - + +
29B THR* 3.5 25.6 - - + -
32B GLU* 2.7 41.5 + - + +
36B ARG* 3.5 25.6 - - - -
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Residues in contact with PHE 10 (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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6B LEU 3.1 15.1 + - - +
7B ILE* 4.0 9.6 - - + +
8B GLU 2.8 1.0 + - - -
9B TYR* 1.3 78.7 - - - +
11B LYS* 1.3 68.6 + - + +
13B GLN* 3.8 8.6 - - - +
14B MSE 3.9 26.0 + - - +
22B SER* 3.7 6.5 - - - -
25B ALA* 3.5 12.6 - - + -
26B ALA* 3.2 35.2 - - + -
29B THR* 3.4 28.9 - - + +
57B CYS* 4.2 22.7 - - + -
60B ASP* 4.4 28.3 - - + -
65B VAL* 4.5 7.4 - - + -
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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
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7B ILE* 3.3 26.4 + - + +
8B GLU* 2.7 12.6 + - - +
10B PHE* 1.3 77.9 - - + +
12B SER* 1.3 61.7 + - - +
14B MSE 3.5 6.8 + - - +
15B LYS* 3.3 28.9 + - + +
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Residues in contact with SER 12 (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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8B GLU 2.9 10.9 + - - -
9B TYR* 3.1 19.2 + - - -
11B LYS* 1.3 74.5 - - - +
13B GLN* 1.3 67.8 + - - +
14B MSE 3.0 2.2 - - - -
15B LYS* 2.8 24.1 + - - +
16B GLU* 2.9 16.7 + - - +
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Residues in contact with GLN 13 (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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9B TYR* 2.9 61.8 + - + +
10B PHE* 3.8 9.0 - - - +
12B SER* 1.3 79.9 + - - +
14B MSE 1.3 58.9 + - - +
16B GLU* 4.1 12.2 + - - +
17B ASP* 3.8 18.0 + - - +
20B MSE 4.1 8.6 - - - +
25B ALA* 4.2 15.0 - - + +
28B ARG* 2.9 36.3 + - + +
29B THR* 3.8 8.1 - - + -
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Residues in contact with MSE 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 PHE* 3.9 23.1 + - - +
11B LYS* 3.5 8.4 + - - +
12B SER 3.0 0.6 - - - -
13B GLN* 1.3 75.7 - - - +
15B LYS* 1.3 63.0 + - - +
17B ASP 2.8 30.9 - - - +
18B PRO* 3.1 12.2 - - + +
20B MSE 3.8 12.3 - - - +
22B SER* 3.5 36.1 - - - +
25B ALA* 3.3 28.0 - - + -
60B ASP* 5.7 1.1 - - - +
62B SER* 5.8 0.2 - - - +
132B ARG* 4.8 5.2 - - - +
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Residues in contact with LYS 15 (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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11B LYS* 3.3 22.3 + - + +
12B SER* 2.8 17.2 + - - +
14B MSE 1.3 74.5 - - - +
16B GLU* 1.3 56.8 + - - +
17B ASP 2.9 9.8 + - - -
18B PRO* 3.8 12.1 - - - +
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Residues in contact with GLU 16 (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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12B SER 2.9 13.2 + - - +
13B GLN* 4.5 12.2 + - - +
15B LYS* 1.3 75.6 - - - +
17B ASP* 1.3 63.2 + - - +
18B PRO* 4.2 1.7 - - - +
28B ARG* 5.8 1.7 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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