Contacts of the helix formed by residues 5 - 20 (chain F) in PDB entry 3EXF
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 VAL 5 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F THR* 1.3 70.7 - - - +
6F ARG* 1.3 65.2 + - - +
8F ALA* 3.3 3.5 + - - +
9F ILE* 3.1 27.7 + - + +
147F PRO* 6.2 1.8 - - + -
148F TRP 3.7 22.4 - - - +
149F ASN 3.8 16.6 - - - -
150F SER* 3.7 6.1 - - - +
153F ALA* 4.3 15.4 - - + +
171F GLU* 6.4 0.7 - - + -
172F ASN 6.2 0.9 - - - +
175F MET* 3.3 28.3 - - + +
176F TYR* 2.9 22.2 + - + +
178F VAL 3.2 9.6 + - - +
180F PHE* 4.1 7.2 - - + -
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Residues in contact with ARG 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F THR* 4.3 5.2 + - - +
5F VAL* 1.3 80.1 - - - +
7F ASP* 1.3 68.7 + - - +
9F ILE* 3.4 7.0 + - - +
10F ASN* 3.2 19.2 + - + +
37F TYR* 2.9 26.4 + - - +
38F LYS* 4.1 17.9 - - - +
39F VAL* 4.3 10.7 - - + +
41F ARG* 3.5 25.1 - - - +
173F GLU* 5.4 2.6 + - - -
176F TYR* 2.8 46.0 + - + +
177F GLY* 3.5 25.9 - - - +
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Residues in contact with ASP 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F VAL* 4.2 13.2 - - + +
4F THR* 2.8 33.2 + - - +
6F ARG* 1.3 75.8 - - - +
8F ALA* 1.3 59.5 + - - +
10F ASN* 3.0 8.5 + - + +
11F GLN* 2.8 40.2 + - + +
41F ARG* 3.7 21.7 + - - -
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Residues in contact with ALA 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F VAL* 4.0 5.2 - - + +
4F THR 2.9 15.0 + - - +
5F VAL 3.7 3.6 - - - +
7F ASP* 1.3 73.1 - - - +
9F ILE* 1.3 67.8 + - - +
11F GLN* 3.7 3.5 + - - -
12F GLY 3.3 14.7 + - - -
150F SER* 3.3 39.3 - - - +
153F ALA* 4.4 1.1 - - + -
154F LYS* 3.4 20.0 - - - +
182F PHE* 3.9 15.7 - - + -
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Residues in contact with ILE 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 3.1 21.4 + - + +
6F ARG* 3.8 4.0 - - - +
7F ASP 3.3 0.2 - - - -
8F ALA* 1.3 73.8 - - - +
10F ASN* 1.3 59.4 + - - +
12F GLY* 3.1 5.0 + - - -
13F MET* 2.9 40.5 + - - +
39F VAL* 3.9 22.7 - - + -
115F ARG* 4.5 0.9 - - - +
147F PRO* 6.4 1.1 - - + -
153F ALA* 3.8 17.9 - - + +
157F ILE* 4.1 22.0 - - + +
171F GLU* 4.0 27.4 - - + +
176F TYR* 3.8 28.9 - - + -
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Residues in contact with ASN 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ARG* 3.2 8.1 + - + +
7F ASP* 3.0 13.3 + - + +
9F ILE* 1.3 74.3 - - - +
11F GLN* 1.3 64.9 + - - +
13F MET* 3.3 6.3 + - - +
14F ASP* 2.7 38.3 + - - +
39F VAL 2.9 26.8 + - - +
40F SER* 3.4 4.9 - - - +
41F ARG* 3.2 19.0 + - - +
43F LEU* 3.2 28.3 - - - +
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Residues in contact with GLN 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F VAL* 4.6 19.4 - - - +
7F ASP* 2.8 28.1 + - + +
8F ALA 4.0 3.4 - - - +
10F ASN* 1.3 75.5 + - - +
12F GLY* 1.3 54.9 + - - +
14F ASP* 3.4 8.6 - - - +
15F GLU* 2.7 50.8 + - - +
154F LYS* 3.1 26.0 + - - +
182F PHE* 3.8 15.9 - - - -
187F GLN* 5.2 3.0 - - - +
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Residues in contact with GLY 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ALA 3.3 5.6 + - - -
9F ILE 3.1 7.8 + - - -
11F GLN* 1.3 78.6 - - - +
13F MET* 1.3 62.4 + - - -
15F GLU* 3.1 3.4 + - - +
16F GLU* 2.9 24.7 + - - +
154F LYS* 3.8 13.1 - - - +
157F ILE* 4.1 7.4 - - - -
158F LYS* 3.9 24.0 - - - -
161F ILE* 5.0 0.2 - - - -
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Residues in contact with MET 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 2.9 19.3 + - + +
10F ASN* 3.9 9.9 - - - +
12F GLY* 1.3 70.5 - - - -
14F ASP* 1.3 64.6 + - - +
16F GLU* 3.0 3.3 + - - +
17F LEU* 2.9 33.0 + - + +
25F LEU* 4.7 9.4 - - + -
39F VAL* 3.8 26.9 - - + +
40F SER* 4.2 7.6 - - - -
43F LEU* 3.5 28.7 - - + -
77F ILE* 4.0 24.9 - - + -
115F ARG* 4.0 31.2 - - - +
157F ILE* 4.6 7.4 - - + +
161F ILE* 4.3 11.4 - - + -
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Residues in contact with ASP 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASN* 2.7 27.7 + - - +
11F GLN* 3.4 7.7 - - - +
13F MET* 1.3 74.8 - - - +
15F GLU* 1.3 63.3 + - - +
17F LEU* 3.2 9.4 + - - -
18F GLU* 3.1 11.3 + - - +
43F LEU* 3.8 18.5 - - + +
46F LYS* 3.2 24.6 + - - +
47F TYR* 3.0 26.2 + - - -
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Residues in contact with GLU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLN* 2.7 34.4 + - - +
12F GLY 3.6 3.5 + - - +
14F ASP* 1.3 75.1 - - - +
16F GLU* 1.3 58.6 + - - +
18F GLU* 3.4 7.1 - - + +
19F ARG* 2.9 31.3 + - - +
154F LYS* 3.0 40.6 + - - -
158F LYS* 3.2 20.8 + - - +
187F GLN 5.0 2.1 - - - +
189F LYS* 3.7 25.4 - - + +
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Residues in contact with GLU 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F GLY 2.9 15.8 + - - +
13F MET 3.7 3.4 - - - +
15F GLU* 1.3 73.6 - - - +
17F LEU* 1.3 67.1 + - - +
19F ARG* 3.0 30.9 + - - -
20F ASP* 3.3 17.8 + - - +
23F VAL* 3.8 11.7 - - + +
158F LYS* 3.2 31.2 + - + +
161F ILE* 3.5 47.8 - - + +
162F ARG* 2.7 32.4 + - - -
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Residues in contact with LEU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F MET* 2.9 29.0 + - + +
14F ASP* 3.2 4.7 + - - +
16F GLU* 1.3 75.5 - - - +
18F GLU* 1.3 69.7 + - - +
19F ARG 3.1 0.2 + - - -
20F ASP 2.9 20.9 - - - +
21F GLU* 4.7 0.2 - - - -
23F VAL* 3.5 35.2 - - + +
24F PHE* 4.1 6.1 - - - -
25F LEU* 5.4 1.8 - - + -
43F LEU* 4.0 18.8 - - + -
47F TYR* 3.5 30.7 - - + -
51F ARG* 3.4 20.2 + - + +
52F ILE* 4.0 22.7 - - + -
77F ILE* 5.4 2.7 - - + -
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Residues in contact with GLU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ASP* 3.1 8.9 + - - +
15F GLU* 3.4 13.9 - - + +
17F LEU* 1.3 79.0 - - - +
19F ARG* 1.3 62.4 + - - +
20F ASP* 3.3 1.6 + - - -
46F LYS* 2.7 36.6 + - - -
47F TYR* 3.3 14.3 + - - -
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Residues in contact with ARG 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLU 2.9 23.6 + - - +
16F GLU* 3.0 20.0 + - - +
17F LEU 3.1 0.4 + - - -
18F GLU* 1.3 73.2 - - - +
20F ASP* 1.3 70.1 + - - +
23F VAL* 6.2 0.2 - - - +
161F ILE* 5.7 1.6 - - - +
162F ARG* 3.2 57.9 - - - +
189F LYS 5.6 2.0 - - - -
190F ASP* 5.6 2.0 + - - -
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Residues in contact with ASP 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLU 3.3 13.4 + - - +
17F LEU 2.9 14.9 + - - +
18F GLU 3.3 1.7 + - - -
19F ARG* 1.3 93.5 + - + +
21F GLU* 1.3 65.4 + - - +
22F LYS* 2.4 28.5 + - - +
23F VAL* 3.6 13.1 + - + +
51F ARG* 3.4 5.4 + - - -
75F ARG* 3.4 22.5 - - - -
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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
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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