Contacts of the helix formed by residues 6 - 21 (chain F) in PDB entry 2GTL
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 6 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E ALA* 4.5 22.4 - - + +
37E ALA* 6.4 1.1 - - + -
5F GLY* 1.3 72.0 - - - +
7F LEU* 1.3 73.7 + - + +
8F GLU* 3.4 2.6 + - - -
9F GLY* 3.2 3.6 + - - -
10F LEU* 2.9 33.6 + - + +
79F LEU 5.7 1.3 - - - +
80F ASP* 6.4 1.6 - - + -
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Residues in contact with LEU 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA 5.0 4.0 - - - +
34E ILE* 5.0 1.6 - - - -
37E ALA* 4.0 25.8 - - + -
122E VAL* 4.2 14.1 - - + -
125E GLN* 3.7 46.6 - - + +
126E VAL* 3.1 33.7 - - + -
6F VAL* 1.3 83.1 - - + +
8F GLU* 1.3 63.0 + - - +
9F GLY 2.7 15.1 + - - -
10F LEU* 2.7 21.0 + - + +
11F LYS* 2.9 11.3 + - - +
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Residues in contact with GLU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E GLN* 4.2 23.0 + - - +
2F LYS* 3.5 28.5 - - + +
3F GLN 2.9 18.4 - - - +
4F CYS* 3.7 5.2 - - - -
5F GLY* 2.9 38.5 - - - +
6F VAL 3.4 5.5 + - - -
7F LEU* 1.3 82.3 + - - +
9F GLY* 1.3 60.3 + - - +
11F LYS* 3.8 5.7 - - - +
12F VAL* 3.1 29.8 + - - +
129F ALA* 4.4 13.6 - - + +
132F ALA* 5.7 0.4 - - + -
133F CYS* 4.2 2.9 - - - -
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Residues in contact with GLY 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F CYS* 4.5 0.7 - - - -
5F GLY 3.6 12.2 + - - -
6F VAL 3.2 6.9 + - - -
7F LEU 2.7 6.1 + - - -
8F GLU* 1.3 73.9 - - - +
10F LEU* 1.3 55.5 + - - -
12F VAL* 2.9 4.2 + - - +
13F LYS* 2.7 37.4 + - - +
79F LEU* 4.2 19.5 - - - +
133F CYS* 4.1 12.8 - - - -
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Residues in contact with LEU 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ARG* 3.5 37.6 + - + +
33E ALA* 4.5 15.7 - - + -
34E ILE* 4.0 27.8 - - + -
126E VAL* 4.2 13.0 - - + +
6F VAL* 2.9 33.9 - - + +
7F LEU* 2.7 15.9 + - + +
9F GLY* 1.3 69.9 - - - +
11F LYS* 1.3 61.3 + - - +
13F LYS* 3.5 10.2 + - + +
14F SER* 3.0 25.5 + - - -
79F LEU 6.3 0.2 - - - -
80F ASP* 4.5 22.0 - - + -
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Residues in contact with LYS 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PRO 3.6 15.8 + - - -
125E GLN* 3.1 30.0 + - - +
126E VAL 3.6 15.9 + - - +
127E LEU* 3.4 25.2 + - - +
128E SER* 3.2 20.3 + - - +
2F LYS* 4.8 4.2 - - - +
7F LEU 2.9 10.0 + - - +
8F GLU* 3.8 8.3 - - - +
10F LEU* 1.3 76.7 - - - +
12F VAL* 1.3 64.7 + - + +
14F SER* 3.1 6.1 + - - -
15F GLU* 2.8 39.2 + - + +
126F ASP* 3.0 37.0 + - + -
129F ALA* 4.3 6.9 - - + +
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F GLU 3.1 15.5 + - - +
9F GLY 2.9 5.8 + - - +
11F LYS* 1.3 75.7 - - - +
13F LYS* 1.3 56.3 + - - +
16F TRP* 2.7 37.6 + - - +
76F ILE* 4.1 17.7 - - + -
79F LEU* 4.5 1.8 - - + -
129F ALA* 3.6 34.8 - - + +
130F TRP* 3.7 42.8 - - + +
133F CYS* 3.8 18.6 - - + -
134F ILE* 5.8 1.3 - - + -
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Residues in contact with LYS 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ARG* 5.9 2.7 - - - +
9F GLY 2.7 21.0 + - - +
10F LEU* 3.7 11.4 - - + +
12F VAL* 1.3 73.8 - - - +
14F SER* 1.3 59.8 + - - +
16F TRP* 3.8 5.4 + - + +
17F GLY* 3.4 14.0 + - - -
76F ILE* 3.6 29.3 - - + +
77F SER* 3.4 28.7 + - - +
79F LEU* 5.2 2.9 - - + +
80F ASP* 2.9 34.2 + - + +
26G THR* 3.8 27.0 - - - +
27G GLU* 3.0 28.9 + - - +
29G SER* 3.6 5.7 + - - +
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Residues in contact with SER 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASP* 4.3 19.3 + - - -
30E ARG* 4.3 19.6 + - - -
126E VAL 5.7 0.4 - - - -
10F LEU 3.0 18.2 + - - -
11F LYS* 3.5 4.7 - - - -
13F LYS* 1.3 74.0 - - - +
15F GLU* 1.3 62.6 - - - +
16F TRP 3.1 1.1 - - - -
17F GLY* 2.8 22.2 + - - -
18F ARG* 3.4 13.8 + - - +
26G THR* 4.3 23.3 - - - +
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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
----------------------------------------------------------
128E SER* 2.8 36.3 + - - +
11F LYS* 2.8 33.0 + - + +
14F SER* 1.3 74.5 - - - +
16F TRP* 1.3 62.3 - - - +
18F ARG* 3.0 29.4 + - - +
19F ALA* 3.0 22.0 + - - +
121F LEU* 3.8 8.3 - - + +
124F CYS 3.7 3.0 - - - +
125F TYR* 3.4 16.3 - - - -
126F ASP 3.4 8.4 + - - -
130F TRP* 2.7 45.1 + - + +
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Residues in contact with TRP 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL 2.7 23.2 + - - +
13F LYS* 3.9 5.6 - - + +
15F GLU* 1.3 72.9 - - - +
17F GLY* 1.3 63.7 + - - +
19F ALA* 4.4 0.9 - - + +
20F TYR* 2.8 65.9 + + + +
29F PHE* 3.8 26.2 - + - -
33F ILE* 5.6 0.2 - - + -
69F LEU* 3.7 20.4 - - + -
72F LEU* 3.6 28.3 - - + -
73F ASP* 3.2 37.7 + - - +
76F ILE* 3.4 31.4 - - + -
77F SER* 5.5 1.8 - - - -
113F ILE* 5.1 2.2 - - + -
117F VAL* 5.0 0.7 - - + -
130F TRP* 3.4 36.2 - + + -
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Residues in contact with GLY 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LYS 3.4 7.8 + - - -
14F SER 2.8 11.0 + - - -
16F TRP* 1.3 87.1 - - - +
18F ARG* 1.3 60.4 + - - +
20F TYR* 4.2 2.4 - - - +
21F GLY* 3.4 16.3 + - - -
26G THR* 6.4 1.6 - - - -
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Residues in contact with ARG 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASP* 4.7 16.0 + - - -
14F SER* 3.4 16.7 + - - +
15F GLU* 3.0 21.7 + - - +
17F GLY* 1.3 78.7 - - - +
19F ALA* 1.3 61.9 + - - +
21F GLY* 3.7 8.1 + - - -
120F GLN* 4.8 2.4 - - - +
121F LEU* 3.7 23.5 + - + +
123F ARG* 3.8 14.5 - - - +
124F CYS* 3.4 45.2 + - - +
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Residues in contact with ALA 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 3.0 14.8 + - - +
16F TRP* 4.0 5.4 - - + +
18F ARG* 1.3 76.2 - - - +
20F TYR* 1.3 66.8 + - - +
21F GLY* 4.5 0.3 - - - -
25F ASP* 5.9 0.2 - - - +
29F PHE* 3.5 26.4 - - + +
117F VAL* 4.0 23.3 - - + -
120F GLN* 3.3 26.4 - - + +
121F LEU* 3.6 16.5 - - + +
130F TRP* 4.8 0.2 - - + -
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Residues in contact with TYR 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 TRP* 2.8 54.4 + + + +
17F GLY* 4.2 3.6 - - - +
19F ALA* 1.3 76.2 - - - +
21F GLY* 1.3 68.1 + - - +
22F SER 3.7 0.2 + - - -
25F ASP* 4.6 1.9 - - - +
26F ARG* 3.2 73.1 + - + -
29F PHE* 4.2 16.3 - + - +
66F ASP 4.3 3.6 + - - -
69F LEU* 4.0 21.0 - - + +
70F GLY* 3.9 20.6 + - - -
73F ASP* 3.6 28.7 - - + +
76G ASN* 5.6 0.5 + - - -
79G ASP* 5.5 0.2 - - - -
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Residues in contact with GLY 21 (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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17F GLY 3.4 13.6 + - - -
18F ARG 4.1 7.6 - - - -
19F ALA 3.4 2.2 - - - -
20F TYR* 1.3 86.7 - - - +
22F SER* 1.3 61.9 + - - -
25F ASP* 5.1 5.4 - - - -
26F ARG* 3.1 19.8 + - - -
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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