Contacts of the helix formed by residues 6 - 21 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA* 5.2 11.4 - - + +
5B GLY* 1.3 72.5 - - - +
7B LEU* 1.3 76.3 + - + +
8B GLU* 3.3 2.8 + - - -
9B GLY* 3.2 2.6 + - - -
10B LEU* 2.8 37.0 + - + +
79B LEU 5.7 1.6 - - - +
80B ASP* 6.4 1.1 - - + -
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Residues in contact with LEU 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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33A ALA* 5.3 1.8 - - + +
34A ILE* 5.6 0.2 - - - -
37A ALA* 3.9 27.4 - - + -
122A VAL* 4.4 10.1 - - + -
125A GLN* 3.3 53.1 - - + +
126A VAL* 3.8 21.5 - - + -
6B VAL* 1.3 83.5 - - + +
8B GLU* 1.3 63.1 + - - +
9B GLY 2.7 16.1 + - - -
10B LEU* 2.7 25.4 + - + +
11B LYS* 2.9 10.9 + - - +
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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
----------------------------------------------------------
125A GLN* 4.4 14.7 + - - -
2B LYS* 3.6 28.5 + - + +
3B GLN 2.9 17.9 - - - +
4B CYS* 3.7 5.2 - - - -
5B GLY* 2.8 38.9 - - - +
6B VAL 3.3 5.5 + - - -
7B LEU* 1.3 81.0 + - - +
9B GLY* 1.3 59.5 + - - +
11B LYS* 3.8 8.3 - - - +
12B VAL* 3.1 30.1 + - - +
129B ALA* 4.3 13.5 - - + +
132B ALA* 5.8 0.2 - - + -
133B CYS* 4.2 2.9 - - - -
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Residues in contact with GLY 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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4B CYS* 4.5 0.7 - - - -
5B GLY 3.7 9.2 + - - -
6B VAL 3.2 7.1 + - - -
7B LEU 2.7 6.1 + - - -
8B GLU* 1.3 74.5 - - - +
10B LEU* 1.3 66.3 + - - -
11B LYS 2.9 2.0 + - - -
12B VAL* 2.9 3.1 + - - +
13B LYS* 2.7 27.4 + - - +
79B LEU* 4.2 18.0 - - - +
133B CYS* 4.1 13.9 - - - -
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Residues in contact with LEU 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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30A ARG* 4.1 24.8 + - + +
33A ALA* 4.2 24.0 - - + -
34A ILE* 4.3 11.4 - - + +
126A VAL* 4.2 26.0 - - + +
6B VAL* 2.8 34.5 - - + +
7B LEU* 2.7 17.9 + - + +
9B GLY* 1.3 71.3 - - - +
11B LYS* 1.3 61.0 + - - +
13B LYS* 3.7 11.0 - - + +
14B SER* 3.0 25.6 + - - -
80B ASP* 4.5 21.5 - - + -
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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
----------------------------------------------------------
124A PRO 3.7 14.6 + - - -
125A GLN* 2.8 41.0 + - - +
126A VAL 3.9 14.7 + - - +
127A LEU* 4.0 10.7 + - - +
128A SER* 3.7 13.3 + - - +
2B LYS* 4.8 5.7 - - - +
7B LEU 2.9 7.3 + - - +
8B GLU* 3.8 9.6 - - - +
10B LEU* 1.3 75.9 - - - +
12B VAL* 1.3 65.8 + - + +
14B SER* 3.0 4.7 + - - -
15B GLU* 2.8 38.5 + - + +
126B ASP* 3.0 47.2 + - + +
129B ALA* 4.3 7.5 - - + +
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Residues in contact with VAL 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 3.1 15.9 + - - +
9B GLY 2.9 5.4 + - - +
11B LYS* 1.3 74.9 - - + +
13B LYS* 1.3 55.5 + - - +
16B TRP* 2.7 37.4 + - - +
76B ILE* 4.2 17.3 - - + -
79B LEU* 4.6 2.0 - - + -
129B ALA* 3.6 34.8 - - + +
130B TRP* 3.7 43.5 - - + +
133B CYS* 3.9 19.3 - - + -
134B ILE* 5.8 1.3 - - + -
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Residues in contact with LYS 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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30A ARG* 6.2 2.2 - - - +
9B GLY 2.7 20.9 + - - +
10B LEU* 3.7 10.8 - - + +
12B VAL* 1.3 74.4 - - - +
14B SER* 1.3 61.4 + - - +
16B TRP* 3.9 5.6 - - + +
17B GLY* 3.4 14.0 + - - -
76B ILE* 3.7 30.2 - - + +
77B SER* 3.4 30.0 + - - +
79B LEU* 5.2 2.9 - - + +
80B ASP* 3.0 37.2 + - + +
26C THR* 4.4 18.0 - - - +
27C GLU* 3.2 29.2 + - - +
28C SER* 6.0 0.4 - - - -
29C SER* 3.5 8.1 + - - +
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 4.7 13.2 + - - -
30A ARG* 3.9 25.9 + - - +
126A VAL 5.2 1.6 - - - -
10B LEU 3.0 17.0 + - - -
11B LYS* 3.5 4.7 - - - -
13B LYS* 1.3 76.4 - - - +
15B GLU* 1.3 63.6 + - - +
17B GLY* 2.8 22.0 + - - -
18B ARG* 3.4 14.9 + - - +
26C THR* 4.4 22.1 - - - +
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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
----------------------------------------------------------
127A LEU* 6.5 0.2 - - - -
128A SER* 2.7 33.2 + - - +
11B LYS* 2.8 33.1 + - + +
14B SER* 1.3 73.7 - - - +
16B TRP* 1.3 63.1 + - - +
18B ARG* 3.1 29.2 + - - +
19B ALA* 3.0 22.0 + - - +
121B LEU* 3.8 8.2 - - + +
124B CYS 3.7 2.4 - - - +
125B TYR* 3.4 18.6 - - - -
126B ASP 3.4 9.6 + - - +
130B TRP* 2.7 43.7 + - + +
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Residues in contact with TRP 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 VAL 2.7 22.1 + - - +
13B LYS* 3.9 5.2 - - + +
15B GLU* 1.3 73.9 - - - +
17B GLY* 1.3 63.7 + - - +
19B ALA* 3.2 0.8 + - - +
20B TYR* 2.8 68.0 + + + +
29B PHE* 3.7 26.2 - + - -
69B LEU* 3.7 20.0 - - + -
72B LEU* 3.7 28.3 - - + -
73B ASP* 3.2 37.9 + - - +
76B ILE* 3.4 32.3 - - + -
77B SER* 5.5 1.6 - - - -
113B ILE* 5.0 2.0 - - + -
117B VAL* 4.9 0.7 - - + -
130B TRP* 3.4 35.8 - + + -
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Residues in contact with GLY 17 (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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13B LYS 3.4 7.7 + - - -
14B SER 2.8 11.0 + - - -
16B TRP* 1.3 87.7 - - - +
18B ARG* 1.3 59.9 + - - +
20B TYR* 4.2 2.3 - - - +
21B GLY* 3.4 17.2 + - - -
26C THR* 6.2 3.4 - - - -
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Residues in contact with ARG 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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21A ASP* 4.8 17.6 + - - -
128A SER* 5.7 2.2 + - - +
14B SER* 3.4 16.0 + - - +
15B GLU* 3.1 21.9 + - - +
17B GLY* 1.3 77.2 - - - +
19B ALA* 1.3 64.9 + - - +
21B GLY* 3.7 8.1 + - - -
120B GLN* 4.8 2.6 - - - +
121B LEU* 3.6 23.1 + - + +
123B ARG* 3.8 14.6 - - - +
124B CYS* 3.4 44.3 + - - +
65M HIS* 5.8 2.3 + - - -
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Residues in contact with ALA 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 3.0 15.4 + - - +
16B TRP* 3.9 5.2 - - - +
18B ARG* 1.3 75.7 - - - +
20B TYR* 1.3 67.9 + - - +
21B GLY* 4.4 0.2 - - - -
25B ASP* 5.9 0.2 - - - +
29B PHE* 3.6 25.9 - - + -
117B VAL* 4.0 22.9 - - + -
120B GLN* 3.3 27.1 - - + +
121B LEU* 3.6 16.5 - - + +
130B TRP* 4.8 0.2 - - + -
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Residues in contact with TYR 20 (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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16B TRP* 2.8 56.6 + + + +
17B GLY* 4.2 3.1 - - - +
19B ALA* 1.3 75.0 - - - +
21B GLY* 1.3 68.8 + - - +
22B SER 3.7 0.3 + - - -
25B ASP* 4.6 1.6 - - - +
26B ARG* 3.2 74.3 + - + -
29B PHE* 4.2 16.1 - + - +
66B ASP 4.3 3.5 + - - -
69B LEU* 4.0 21.8 - - + +
70B GLY* 3.9 21.7 + - - -
73B ASP* 3.7 28.3 - - + -
76C ASN* 5.4 1.4 + - - -
79C ASP* 5.8 0.2 - - - -
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Residues in contact with GLY 21 (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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17B GLY 3.4 13.9 + - - -
18B ARG 3.7 7.2 + - - -
19B ALA 3.4 1.8 - - - -
20B TYR* 1.3 86.6 - - - +
22B SER* 1.3 61.1 + - - -
25B ASP* 5.1 5.6 - - - -
26B ARG* 3.1 20.8 + - - -
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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
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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