Contacts of the helix formed by residues 2 - 15 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A CXM 1.3 72.4 - - - +
3A GLN* 1.3 74.0 + - + +
5A LEU* 3.3 4.0 + - - +
6A GLU* 2.9 59.2 + - + +
224A PRO* 3.9 15.1 - - + +
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Residues in contact with GLN 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CXM 3.9 9.2 - - - +
2A LYS* 1.3 88.6 + - + +
4A TYR* 1.3 62.1 + - - +
6A GLU* 3.4 13.5 + - - +
7A LEU 3.2 17.2 + - - -
32A HIS* 5.3 1.0 - - - -
34A MET* 3.6 32.5 - - + +
35A ARG 2.9 28.0 + - - +
36A PHE* 3.4 26.4 - - + +
37A ASN 5.3 0.4 - - - +
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Residues in contact with TYR 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CXM 3.0 30.6 + - + +
3A GLN* 1.3 76.3 - - - +
5A LEU* 1.3 76.7 + - + +
7A LEU* 3.3 4.4 + - - +
8A MET* 3.0 38.6 + - + +
34A MET* 4.3 8.9 - - + -
36A PHE* 5.0 0.8 - - + -
45A VAL* 4.0 17.5 - - + -
48A LYS* 5.1 0.2 + - - -
170A VAL* 2.5 37.2 + - + -
171A PHE* 3.5 15.2 + - - -
174A LEU* 3.9 26.7 - - + -
175A PRO* 3.5 17.3 - - + +
178A ILE* 4.5 5.8 - - + -
219A GLN* 3.6 24.9 + - - -
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Residues in contact with LEU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CXM 2.8 23.4 + - - +
2A LYS* 3.9 4.3 - - - +
4A TYR* 1.3 87.3 - - + +
6A GLU* 1.3 55.9 + - - +
8A MET* 3.1 12.7 + - - +
9A GLN* 2.7 37.4 + - - +
47A THR* 3.9 17.3 - - + +
219A GLN* 4.2 18.2 - - + +
220A LEU* 3.7 15.4 - - + +
222A ARG 3.6 24.5 - - - +
224A PRO* 3.8 23.1 - - + -
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 2.9 51.1 + - + +
3A GLN* 3.7 12.2 - - - +
4A TYR 3.3 0.2 - - - -
5A LEU* 1.3 76.0 - - + +
7A LEU* 1.3 58.8 + - - +
9A GLN* 3.3 6.5 + - - +
10A LYS* 2.8 30.7 + - - +
32A HIS* 5.6 1.1 - - - +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN 3.2 10.7 + - - +
4A TYR 3.6 7.0 - - - +
5A LEU 3.2 0.2 - - - -
6A GLU* 1.3 77.6 - - - +
8A MET* 1.3 65.8 + - - +
10A LYS* 3.2 4.2 + - + -
11A VAL* 2.9 37.1 + - + +
29A ILE* 4.0 8.5 - - + -
32A HIS* 3.7 39.6 + - + +
34A MET* 4.1 11.0 - - + -
170A VAL* 4.0 15.9 - - + -
174A LEU* 3.5 32.8 - - + -
201A TRP* 4.2 8.5 - - + -
206A THR* 4.0 11.2 - - + -
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Residues in contact with MET 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.0 41.5 + - + +
5A LEU* 3.5 17.3 - - - +
7A LEU* 1.3 78.2 - - - +
9A GLN* 1.3 61.8 + - - +
11A VAL* 3.3 5.0 + - - +
12A LEU* 3.1 22.7 + - - +
170A VAL* 4.3 13.7 - - + +
171A PHE* 3.7 22.2 - - + -
208A LEU* 3.8 8.8 - - + +
216A THR* 3.6 36.3 - - + +
219A GLN* 3.6 22.7 - - - +
220A LEU* 4.0 16.4 - - + -
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Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU 2.7 20.6 + - - +
6A GLU* 3.6 8.3 - - - +
8A MET* 1.3 71.3 - - - +
10A LYS* 1.3 52.7 + - - +
12A LEU* 3.2 20.7 + - - +
13A ASP* 2.7 72.7 + - - +
220A LEU* 3.7 25.1 - - + +
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLU 2.8 21.1 + - - +
7A LEU* 3.5 6.5 - - + +
9A GLN* 1.3 74.2 - - - +
11A VAL* 1.3 54.9 + - - +
13A ASP* 4.5 4.5 - - - -
14A GLU* 2.6 77.7 + - + +
29A ILE* 4.2 17.0 - - + +
31A GLY 5.8 1.8 - - - -
32A HIS* 3.9 30.5 - - + +
35B ARG* 5.8 4.9 - - - +
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 2.9 38.4 + - + +
8A MET* 3.8 4.9 - - - +
10A LYS* 1.3 75.8 - - - +
12A LEU* 1.3 59.4 + - - +
15A GLY* 2.9 25.4 + - - +
27A LEU* 3.1 35.4 - - + +
28A SER* 4.6 1.6 - - - -
29A ILE* 4.0 16.8 - - + -
170A VAL* 4.4 11.9 - - + -
206A THR* 4.1 11.4 - - + +
207A HIS* 4.3 0.9 - - - -
208A LEU* 3.7 26.2 - - + +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET 3.1 13.1 + - - +
9A GLN* 3.4 17.9 - - - +
11A VAL* 1.3 81.4 - - - +
13A ASP* 1.3 65.9 + - - +
15A GLY 4.4 2.6 + - - +
27A LEU* 4.1 17.5 - - + +
208A LEU* 4.2 4.2 - - + +
213A MET* 3.9 29.4 - - + -
216A THR* 4.5 6.3 - - + -
217A HIS* 3.8 28.9 - - + +
220A LEU* 3.5 28.3 - - + -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLN* 2.7 53.6 + - - +
10A LYS* 3.9 2.9 - - - +
12A LEU* 1.3 80.1 - - - +
14A GLU* 1.3 68.2 + - + +
15A GLY 5.2 0.6 - - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 2.6 60.8 + - + +
13A ASP* 1.3 82.5 - - + +
15A GLY* 1.3 61.8 + - - +
16A THR* 3.8 3.5 + - - -
29A ILE* 4.1 10.1 - - + +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS 3.6 1.8 + - - -
11A VAL 2.9 22.9 + - - +
12A LEU 4.4 1.9 + - - +
13A ASP 3.8 1.7 - - - +
14A GLU* 1.3 79.1 - - - +
16A THR* 1.3 62.6 + - - -
17A GLN 4.0 0.9 + - - -
27A LEU* 4.1 10.3 - - - +
28A SER 3.5 16.2 - - - -
29A ILE* 3.7 9.1 - - - +
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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