Contacts of the helix formed by residues 5 - 20 (chain L) in PDB entry 3EXG
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L THR* 1.3 72.0 - - - +
6L ARG* 1.3 67.0 + - - +
8L ALA* 2.8 15.5 + - - +
9L ILE* 2.9 22.9 + - + +
147L PRO* 6.3 0.2 - - + -
148L TRP 4.2 9.9 - - - +
149L ASN* 3.9 5.8 - - - +
150L SER* 3.5 25.1 + - - +
153L ALA* 3.7 25.1 - - + -
175L MET* 3.3 35.0 - - + +
176L TYR* 3.5 5.0 + - + -
178L VAL 3.1 10.5 + - - +
180L PHE* 4.3 5.6 - - + -
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Residues in contact with ARG 6 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L THR* 4.0 5.6 + - - +
5L VAL* 1.3 81.6 - - - +
7L ASP* 1.3 70.8 + - - +
9L ILE* 3.5 4.2 + - - +
10L ASN* 3.2 20.0 + - + +
37L TYR* 2.7 29.3 + - - +
38L LYS* 3.6 26.1 - - - +
39L VAL* 4.0 11.2 - - + +
41L ARG* 4.0 14.1 - - - +
176L TYR* 3.1 64.6 + - + +
177L GLY* 4.0 9.3 - - - +
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Residues in contact with ASP 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L VAL* 4.6 8.8 - - + +
4L THR* 3.1 32.9 + - - +
6L ARG* 1.3 87.8 - - - +
8L ALA* 1.3 59.0 + - - +
10L ASN* 3.4 7.7 + - - +
11L GLN* 2.9 33.9 + - - +
41L ARG* 4.7 7.3 + - - -
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Residues in contact with ALA 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L VAL* 4.3 8.0 - - + +
4L THR 2.9 13.3 + - - +
5L VAL* 2.8 10.2 + - - +
7L ASP* 1.3 77.5 - - - +
9L ILE* 1.3 62.5 + - - +
11L GLN* 3.1 10.0 + - - +
12L GLY 3.0 18.4 + - - -
150L SER* 3.6 36.8 - - - +
153L ALA* 4.8 0.9 - - + -
154L LYS* 3.7 19.7 - - + +
182L PHE* 4.6 2.9 - - + -
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Residues in contact with ILE 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L VAL* 2.9 22.4 + - + +
6L ARG 3.9 4.3 - - - +
8L ALA* 1.3 74.1 - - - +
10L ASN* 1.3 58.1 + - - +
12L GLY* 3.3 1.9 + - - -
13L MET* 2.8 37.0 + - + +
39L VAL* 3.9 18.2 - - + -
115L ARG* 4.1 7.2 - - - +
147L PRO* 5.8 0.4 - - + -
153L ALA* 3.8 28.3 - - + +
154L LYS* 4.7 0.2 - - - +
157L ILE* 4.4 11.8 - - + +
171L GLU* 3.5 40.2 - - + +
176L TYR* 3.7 23.3 - - + -
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Residues in contact with ASN 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L ARG* 3.2 10.0 + - + +
7L ASP* 3.5 12.7 - - - +
8L ALA 3.1 0.4 - - - -
9L ILE* 1.3 79.0 - - - +
11L GLN* 1.3 66.1 + - - +
13L MET* 3.0 9.2 + - - +
14L ASP* 2.8 27.0 + - - +
38L LYS 5.1 0.6 + - - +
39L VAL 2.8 29.7 + - - +
40L SER 3.6 3.2 - - - -
41L ARG* 3.2 33.3 + - - +
43L LEU* 3.8 15.2 - - - +
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Residues in contact with GLN 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L VAL* 4.7 10.5 - - - +
7L ASP* 2.9 15.4 + - - +
8L ALA* 3.3 11.0 - - - +
10L ASN* 1.3 77.4 + - - +
12L GLY* 1.3 62.4 + - - +
14L ASP* 3.4 7.4 + - - +
15L GLU* 3.0 39.2 + - + +
154L LYS* 2.5 34.0 + - + +
182L PHE* 3.7 24.1 - - - -
187L GLN* 3.8 10.3 - - - +
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Residues in contact with GLY 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L ALA 3.0 10.3 + - - -
9L ILE 3.7 2.2 - - - -
11L GLN* 1.3 77.2 - - - +
13L MET* 1.3 68.0 + - - +
15L GLU* 3.2 3.5 + - - +
16L GLU* 3.2 27.2 + - - +
154L LYS* 4.0 2.8 - - - +
157L ILE* 4.2 7.4 - - - -
158L LYS* 3.7 31.3 - - - +
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Residues in contact with MET 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L ILE* 2.8 15.3 + - + +
10L ASN* 3.5 8.5 - - - +
12L GLY* 1.3 76.6 - - - +
14L ASP* 1.3 64.1 + - - +
16L GLU* 3.5 2.8 + - - +
17L LEU* 3.2 31.8 + - + +
25L LEU* 3.9 23.8 - - + -
39L VAL* 3.7 39.7 - - + +
40L SER* 4.0 4.0 - - - -
43L LEU* 3.9 20.6 - - + -
77L ILE* 4.4 16.6 - - + -
115L ARG* 4.0 24.9 - - - +
157L ILE* 4.2 17.3 - - + +
161L ILE* 4.6 9.0 - - - +
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Residues in contact with ASP 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L ASN* 2.8 16.5 + - - +
11L GLN* 3.4 13.9 - - + +
13L MET* 1.3 77.3 - - - +
15L GLU* 1.3 65.7 + - + +
17L LEU* 3.2 14.1 + - - +
18L GLU* 3.2 5.0 + - - +
43L LEU* 4.4 18.3 - - + +
46L LYS* 3.0 21.1 + - - +
47L TYR* 2.6 43.1 + - - -
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Residues in contact with GLU 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L GLN* 3.0 26.7 + - + +
12L GLY 3.2 1.5 + - - +
14L ASP* 1.3 79.3 - - + +
16L GLU* 1.3 59.3 + - - +
18L GLU* 3.2 11.4 + - - +
19L ARG* 2.9 28.9 + - - +
154L LYS* 3.2 31.8 + - - -
158L LYS* 3.1 25.5 + - - +
187L GLN 4.0 3.8 - - - +
188L SER 3.7 4.7 - - - +
189L LYS* 3.7 37.0 - - + +
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Residues in contact with GLU 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L GLY 3.2 13.4 + - - +
13L MET 3.6 7.0 - - - +
15L GLU* 1.3 79.1 - - - +
17L LEU* 1.3 56.5 + - - +
19L ARG* 3.3 16.7 + - - +
20L ASP* 3.0 32.2 + - - +
23L VAL* 4.6 5.0 - - + +
158L LYS* 2.7 31.8 + - - +
161L ILE* 3.6 39.9 - - + +
162L ARG* 2.5 48.0 + - - -
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Residues in contact with LEU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L MET* 3.2 23.8 + - + +
14L ASP 3.2 9.2 + - - +
16L GLU* 1.3 75.6 - - - +
18L GLU* 1.3 65.1 + - - +
20L ASP 3.3 4.6 - - - +
21L GLU* 4.7 0.2 - - - -
23L VAL* 3.1 38.6 - - + +
24L PHE* 4.5 4.5 - - - -
25L LEU* 5.5 4.7 - - + -
43L LEU* 4.3 14.8 - - + -
47L TYR* 3.6 34.0 - - + -
51L ARG* 2.8 51.4 + - + +
52L ILE* 4.6 8.7 - - + -
77L ILE* 5.4 4.9 - - + -
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Residues in contact with GLU 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L ASP* 3.2 9.7 + - - +
15L GLU* 3.7 11.4 - - - +
16L GLU 3.2 0.4 - - - -
17L LEU* 1.3 77.3 - - - +
19L ARG* 1.3 68.6 + - - +
20L ASP* 3.1 2.6 + - - -
21L GLU* 4.8 0.9 + - - +
46L LYS* 3.7 28.6 + - - -
47L TYR* 3.8 10.2 + - + +
189L LYS* 6.4 0.7 - - - -
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Residues in contact with ARG 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L GLU 2.9 17.7 + - - +
16L GLU* 3.4 23.3 + - - +
18L GLU* 1.3 78.1 - - - +
20L ASP* 1.3 73.1 + - + +
75L ARG* 5.9 2.0 - - - +
161L ILE* 5.8 2.0 - - - +
162L ARG* 3.4 55.9 - - - +
189L LYS* 4.6 21.5 - - - +
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Residues in contact with ASP 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L GLU 3.0 11.8 + - - +
17L LEU 3.3 3.3 - - - +
18L GLU 3.1 1.0 + - - -
19L ARG* 1.3 95.8 + - - +
21L GLU* 1.3 62.9 + - - +
22L LYS* 2.7 38.0 + - - +
23L VAL* 3.3 17.6 + - + +
51L ARG* 3.0 15.6 + - - -
75L ARG* 3.4 23.0 + - - -
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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
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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