Contacts of the helix formed by residues 2 - 15 (chain B) in PDB entry 1JG0
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 LYS 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 CXM 1.3 72.4 - - - +
3B GLN* 1.3 68.2 + - + +
5B LEU* 3.2 3.9 + - - +
6B GLU* 2.9 49.5 + - + +
224B PRO* 4.0 13.6 - - + +
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Residues in contact with GLN 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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1B CXM 3.4 1.8 - - - +
2B LYS* 1.3 82.8 - - + +
4B TYR* 1.3 62.3 + - - +
6B GLU* 3.4 18.0 + - - +
7B LEU* 3.0 17.3 + - - +
32B HIS* 5.2 1.0 - - - -
33B GLN 4.9 0.2 - - - +
34B MET* 3.4 31.9 - - + +
35B ARG* 2.4 51.2 + - - +
36B PHE* 4.0 18.0 - - + -
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Residues in contact with TYR 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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1B CXM 2.9 30.5 + - + +
3B GLN* 1.3 77.2 - - - +
5B LEU* 1.3 75.1 + - + +
7B LEU* 3.2 6.0 + - + +
8B MET* 3.1 36.4 + - + +
34B MET* 4.2 7.8 - - + -
36B PHE* 5.1 0.8 - - - -
45B VAL* 4.0 17.7 - - + -
48B LYS* 5.0 0.2 + - - -
170B VAL* 2.5 38.4 + - + -
171B PHE* 3.4 14.2 + - - -
174B LEU* 3.7 29.8 - - + -
175B PRO* 3.5 19.6 - - + +
178B ILE* 4.7 7.0 - - + -
219B GLN* 3.7 24.5 + - - -
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Residues in contact with LEU 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 CXM 2.8 16.6 + - - +
2B LYS* 3.8 4.0 - - - +
4B TYR* 1.3 84.0 - - + +
6B GLU* 1.3 66.9 + - + +
8B MET* 3.2 11.8 + - - +
9B GLN* 3.0 23.8 + - - +
47B THR* 3.8 20.2 - - + +
219B GLN* 4.3 12.1 - - + +
220B LEU* 3.7 27.1 - - + +
222B ARG 3.9 11.7 - - - +
224B PRO* 3.3 38.8 - - + -
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Residues in contact with GLU 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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2B LYS* 2.9 53.2 + - + +
3B GLN* 3.7 18.0 - - - +
5B LEU* 1.3 77.1 - - + +
7B LEU* 1.3 58.7 + - - +
9B GLN* 3.3 7.7 + - - +
10B LYS* 2.9 30.4 + - - +
32B HIS* 5.7 1.6 - - + +
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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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3B GLN 3.0 13.6 + - - +
4B TYR 3.4 9.2 - - - +
5B LEU 3.2 0.2 - - - -
6B GLU* 1.3 77.2 - - - +
8B MET* 1.3 62.7 + - - +
10B LYS* 3.2 4.8 + - + +
11B VAL* 2.9 26.2 + - + +
29B ILE* 4.0 15.5 - - + -
32B HIS* 3.5 43.7 - - + +
34B MET* 4.0 14.1 - - + -
170B VAL* 4.2 11.4 - - + -
174B LEU* 3.4 32.3 - - + -
201B TRP* 4.3 2.9 - - + -
206B THR* 4.1 16.4 - - + -
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Residues in contact with MET 8 (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 TYR* 3.1 39.4 + - + +
5B LEU* 3.2 15.2 + - - +
7B LEU* 1.3 75.4 - - - +
9B GLN* 1.3 63.8 + - - +
11B VAL* 3.3 3.7 + - - +
12B LEU* 3.0 27.3 + - - +
170B VAL* 3.8 16.8 - - + -
171B PHE* 3.7 27.1 - - + -
208B LEU* 3.8 10.4 - - + +
216B THR* 3.7 32.3 - - + +
219B GLN* 3.6 25.4 - - - +
220B LEU* 4.0 18.8 - - + -
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Residues in contact with GLN 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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5B LEU 3.0 16.0 + - - +
6B GLU* 3.5 7.6 - - - +
8B MET* 1.3 77.2 - - - +
10B LYS* 1.3 57.5 + - - +
12B LEU* 3.1 17.9 + - - +
13B ASP* 2.8 68.4 + - - +
220B LEU* 3.8 21.9 - - + +
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Residues in contact with LYS 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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35A ARG* 5.4 5.1 - - - +
6B GLU 2.9 17.2 + - - +
7B LEU* 3.5 6.7 - - + +
9B GLN* 1.3 72.2 - - - +
11B VAL* 1.3 61.2 + - - +
13B ASP* 4.4 5.2 - - - +
14B GLU* 2.7 63.2 + - + +
29B ILE* 4.3 15.0 - - + +
31B GLY 5.2 3.6 + - - -
32B HIS* 3.6 36.0 + - + +
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Residues in contact with VAL 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 LEU* 2.9 26.2 + - + +
8B MET* 3.7 7.0 - - - +
10B LYS* 1.3 75.9 - - - +
12B LEU* 1.3 59.7 + - - +
15B GLY* 2.8 27.2 + - - +
27B LEU* 3.5 35.0 - - + +
28B SER* 4.5 2.0 - - - +
29B ILE* 4.1 28.5 - - + -
170B VAL* 4.4 14.1 - - + -
206B THR 4.1 6.5 - - - +
207B HIS* 4.4 0.9 - - - -
208B LEU* 3.6 27.4 - - + +
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Residues in contact with LEU 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 MET 3.0 12.7 + - - +
9B GLN* 3.2 18.8 - - - +
10B LYS 3.1 0.2 - - - -
11B VAL* 1.3 79.7 - - - +
13B ASP* 1.3 68.7 + - - +
15B GLY 4.3 2.3 + - - +
27B LEU* 4.1 18.1 - - + +
208B LEU* 4.3 8.5 - - + -
213B MET* 3.9 28.0 - - - -
216B THR* 4.3 3.8 - - + -
217B HIS* 3.9 27.6 - - + +
220B LEU* 3.3 33.2 - - + -
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Residues in contact with ASP 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 GLN* 2.8 51.3 + - - +
10B LYS* 4.0 3.0 - - - +
12B LEU* 1.3 77.0 - - - +
14B GLU* 1.3 70.5 + - + +
15B GLY 3.8 0.8 - - - +
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Residues in contact with GLU 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 LYS* 2.7 49.5 + - - +
13B ASP* 1.3 85.7 - - + +
15B GLY* 1.3 65.2 + - - +
16B THR* 3.7 4.2 + - - -
28B SER 4.6 0.2 - - - +
29B ILE* 4.1 12.8 - - + +
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Residues in contact with GLY 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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10B LYS 3.7 0.4 + - - -
11B VAL 2.8 23.7 + - - -
12B LEU 4.3 2.1 + - - +
13B ASP 3.8 0.9 - - - +
14B GLU* 1.3 80.2 - - - +
16B THR* 1.3 62.0 - - - -
17B GLN 4.0 1.0 + - - -
27B LEU* 4.1 10.6 - - - +
28B SER 3.3 20.2 - - - -
29B ILE* 3.8 6.0 - - - +
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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