Contacts of the helix formed by residues 6 - 20 (chain C) in PDB entry 1JLH
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 ASP 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ALA 3.3 8.0 + - - +
3C LEU 3.0 17.0 + - - +
4C THR 3.2 0.2 - - - -
5C ARG* 1.3 76.8 - - - +
7C PRO* 1.3 70.6 - - - +
8C GLN* 2.7 35.0 + - - +
9C PHE* 2.9 14.5 + - + +
10C GLN* 3.0 26.3 + - - +
70C LEU* 4.0 9.3 - - - +
73C SER* 2.6 28.3 + - - +
74C ARG* 3.7 17.4 + - - -
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Residues in contact with PRO 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ARG 3.5 7.6 - - - +
6C ASP* 1.3 92.9 - - - +
8C GLN* 1.3 68.5 + - - +
10C GLN* 3.3 14.3 + - + +
11C LYS* 2.9 27.8 + - - +
73C SER* 4.5 5.6 - - - +
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Residues in contact with GLN 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ASP* 2.7 18.8 + - - +
7C PRO* 1.3 80.1 - - + +
9C PHE* 1.3 63.4 + - - +
11C LYS* 3.1 25.5 + - - +
12C LEU* 2.9 25.7 + - - +
66C MET* 4.9 4.2 - - - +
69C ASP* 3.7 27.5 - - + +
70C LEU* 4.0 20.0 - - + +
73C SER* 3.6 21.3 - - - +
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Residues in contact with PHE 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 3.2 64.2 - - + +
4C THR* 3.7 22.9 - - + -
6C ASP* 2.9 16.0 + - + +
8C GLN* 1.3 76.8 - - - +
10C GLN* 1.3 58.7 + - + +
12C LEU* 3.1 11.1 + - + +
13C GLN* 2.9 63.1 + - - +
70C LEU* 4.3 17.2 - - + +
324C ILE* 5.0 4.5 - - + -
328C ASN* 3.8 26.9 - - + -
329C CYS* 5.1 6.1 - - - -
372C HIS* 5.4 4.5 - - + -
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Residues in contact with GLN 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C THR 3.3 22.6 - - - +
5C ARG* 3.9 12.8 - - - +
6C ASP 3.0 14.9 + - - +
7C PRO* 3.6 11.1 + - - +
9C PHE* 1.3 78.6 - - + +
11C LYS* 1.3 58.3 + - - +
13C GLN* 3.2 9.2 + - - +
14C GLN* 2.8 32.2 + - - +
17C ARG* 4.8 1.4 + - - -
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Residues in contact with LYS 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO 2.9 13.8 + - - +
8C GLN* 3.1 30.6 + - - +
10C GLN* 1.3 77.8 - - - +
12C LEU* 1.3 56.3 + - - +
14C GLN* 3.4 6.7 + - - +
15C TRP* 2.9 28.4 + - - +
65C ARG* 3.4 25.9 - - - +
66C MET* 3.8 26.7 - - + +
69C ASP* 4.8 4.2 + - - -
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLN 2.9 10.9 + - - +
9C PHE* 3.3 11.9 - - + +
11C LYS* 1.3 77.4 - - - +
13C GLN* 1.3 56.7 + - - +
15C TRP* 3.2 5.9 + - - +
16C TYR* 2.8 30.0 + - - +
63C VAL* 4.2 5.8 - - + +
66C MET* 3.6 41.1 - - + +
67C LEU* 3.4 30.3 - - + -
70C LEU* 3.7 28.5 - - + -
324C ILE* 5.6 2.0 - - + -
325C TRP* 3.6 34.9 - - + -
329C CYS* 4.7 5.8 - - - -
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Residues in contact with GLN 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C THR* 5.8 1.0 - - - +
9C PHE* 2.9 43.7 + - - +
10C GLN* 3.5 12.2 - - - +
12C LEU* 1.3 78.2 - - - +
14C GLN* 1.3 63.3 + - - +
16C TYR* 3.2 11.2 + - + +
17C ARG* 3.0 53.9 + - + +
328C ASN 3.0 27.5 + - - -
329C CYS* 4.4 10.8 - - - +
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Residues in contact with GLN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLN 2.8 20.1 + - - +
11C LYS* 3.7 7.0 - - - +
13C GLN* 1.3 69.9 - - - +
15C TRP* 1.3 66.9 + - - +
17C ARG* 2.6 40.8 + - - +
18C GLU* 2.5 73.5 + - - +
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Residues in contact with TRP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LYS* 2.9 18.5 + - + +
12C LEU 3.4 4.7 - - - +
14C GLN* 1.3 76.0 - - - +
16C TYR* 1.3 62.2 + - - +
18C GLU* 3.2 3.9 + - - -
19C HIS* 2.9 77.1 + + + -
22C GLU* 4.8 6.1 - - - -
23C LEU* 3.7 31.0 - - + -
60C THR* 4.0 11.9 - - + -
62C ASP* 4.5 12.9 + - + +
63C VAL* 3.5 26.2 - - + -
66C MET* 3.4 32.6 - - + +
325C TRP* 3.9 19.3 - + - -
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Residues in contact with TYR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU 2.8 13.2 + - - +
13C GLN* 3.3 14.4 - - + +
14C GLN 3.2 0.2 - - - -
15C TRP* 1.3 85.3 - - - +
17C ARG* 1.3 72.0 + - + +
20C ARG* 2.8 79.6 + - + +
23C LEU* 5.6 0.2 - - + -
325C TRP* 4.0 14.4 - + + -
329C CYS* 3.2 39.3 + - + -
330C PHE* 3.5 45.9 + + - -
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Residues in contact with ARG 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLN 4.8 1.0 + - - -
13C GLN* 3.0 46.3 + - + +
14C GLN* 2.6 45.1 + - - +
16C TYR* 1.3 90.4 - - + +
18C GLU* 1.3 61.1 + - - +
20C ARG* 4.5 4.5 + - - +
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLN* 2.5 49.0 + - - +
15C TRP* 3.2 1.1 + - - -
17C ARG* 1.3 80.4 - - + +
19C HIS* 1.3 87.2 + - + +
20C ARG 3.7 0.2 - - - -
21C SER* 5.6 1.9 + - - -
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Residues in contact with HIS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 2.9 66.8 + + + +
16C TYR 3.8 0.2 - - - -
18C GLU* 1.3 100.6 - - + +
20C ARG* 1.3 67.7 + - - +
21C SER* 3.4 2.7 - - - -
22C GLU* 2.8 56.0 + - - +
23C LEU* 3.7 6.2 + - - +
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 2.8 68.1 + - + +
17C ARG* 4.5 4.9 + - - +
18C GLU 3.7 1.6 - - - -
19C HIS* 1.3 71.1 - - - +
21C SER* 1.3 55.8 + - - +
22C GLU 2.7 11.3 + - - -
23C LEU* 3.0 28.5 + - - +
330C PHE* 3.5 32.0 + - + -
400C MET* 5.0 5.1 - - - -
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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