Contacts of the helix formed by residues 6 - 20 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ALA 3.2 9.6 + - - +
3D LEU 3.0 16.4 + - - +
4D THR 3.2 0.4 - - - -
5D ARG* 1.3 76.9 - - - +
7D PRO* 1.3 64.1 - - - +
8D GLN* 2.9 32.4 + - - +
9D PHE* 3.0 13.9 + - + +
10D GLN* 2.9 31.1 + - - +
70D LEU* 3.4 12.4 - - - +
73D SER* 2.6 27.4 + - - +
74D ARG* 3.5 17.7 + - - -
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Residues in contact with PRO 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ARG 3.4 7.6 - - - +
6D ASP* 1.3 89.8 - - - +
8D GLN* 1.3 76.4 + - - +
10D GLN* 3.3 14.3 + - + +
11D LYS* 2.9 28.8 + - - +
73D SER* 4.5 0.9 - - - +
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Residues in contact with GLN 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASP* 2.9 9.7 + - - +
7D PRO* 1.3 93.3 - - - +
9D PHE* 1.3 64.6 + - - +
11D LYS* 3.4 14.2 + - + +
12D LEU* 3.1 25.8 + - - +
66D MET* 4.8 2.2 - - - +
69D ASP* 3.6 33.2 - - + +
70D LEU* 3.8 20.2 - - - +
73D SER* 2.6 28.2 + - - -
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Residues in contact with PHE 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.2 56.1 - - + +
4D THR* 3.8 22.2 - - + -
6D ASP* 3.0 12.0 + - + +
8D GLN* 1.3 74.3 - - - +
10D GLN* 1.3 66.5 + - - +
12D LEU* 3.0 11.2 + - + +
13D GLN* 2.9 62.3 + - + +
70D LEU* 4.2 15.9 - - + +
324D ILE* 5.0 3.8 - - + -
328D ASN* 3.9 34.5 - - + -
329D CYS* 4.5 9.4 - - - -
372D HIS* 5.6 3.8 - - + -
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Residues in contact with GLN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D THR 3.4 23.2 - - - +
5D ARG* 3.6 14.4 - - - +
6D ASP 2.9 20.2 + - - +
7D PRO* 3.6 11.3 - - - +
9D PHE* 1.3 75.8 - - - +
11D LYS* 1.3 63.4 + - - +
13D GLN* 3.3 16.9 + - - +
14D GLN* 3.0 25.6 + - - +
17D ARG* 4.9 1.6 + - - -
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Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PRO 2.9 17.5 + - - +
8D GLN* 3.5 15.0 - - + +
9D PHE 3.1 0.2 - - - -
10D GLN* 1.3 79.0 - - - +
12D LEU* 1.3 61.7 + - - +
14D GLN* 3.5 12.3 + - - +
15D TRP* 3.0 23.2 + - - +
65D ARG* 3.2 32.3 - - - +
66D MET* 3.9 26.1 - - + +
69D ASP* 4.5 6.2 + - + +
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLN 3.1 12.1 + - - +
9D PHE* 3.0 16.2 + - + +
11D LYS* 1.3 76.8 - - - +
13D GLN* 1.3 62.3 + - - +
15D TRP* 3.3 3.6 + - - +
16D TYR* 2.9 23.5 + - - +
63D VAL* 4.3 3.1 - - + +
66D MET* 3.5 42.2 - - + +
67D LEU* 3.6 33.0 - - + +
70D LEU* 4.0 28.9 - - + -
324D ILE* 5.9 1.3 - - + -
325D TRP* 3.8 29.0 - - + -
329D CYS* 4.6 6.5 - - - -
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Residues in contact with GLN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D THR* 4.9 4.6 - - - +
9D PHE* 2.9 56.4 + - + +
10D GLN* 3.3 18.8 + - - +
12D LEU* 1.3 76.7 - - - +
14D GLN* 1.3 63.2 + - - +
16D TYR* 3.0 11.1 + - - +
17D ARG* 2.9 46.8 + - - +
328D ASN 4.7 5.4 + - - +
329D CYS* 4.5 8.5 - - - -
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Residues in contact with GLN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLN 3.0 17.7 + - - +
11D LYS* 3.7 11.1 + - - +
13D GLN* 1.3 75.4 - - - +
15D TRP* 1.3 66.0 + - - +
17D ARG* 3.1 25.8 + - - +
18D GLU* 2.8 53.1 + - - +
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Residues in contact with TRP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LYS 3.0 17.8 + - - +
12D LEU 3.5 4.0 - - - +
14D GLN* 1.3 77.9 - - - +
16D TYR* 1.3 65.8 + - - +
18D GLU* 3.0 3.8 + - - -
19D HIS* 2.8 78.9 + + + -
22D GLU* 5.0 3.8 - - + -
23D LEU* 4.0 34.5 - - + -
60D THR* 4.1 12.8 - - + -
62D ASP* 4.5 12.0 - - + +
63D VAL* 3.4 29.2 - - + -
66D MET* 3.3 30.1 - - + +
325D TRP* 4.0 13.0 - + - -
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Residues in contact with TYR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU 2.9 13.5 + - - +
13D GLN* 3.2 13.9 - - - +
15D TRP* 1.3 86.5 - - - +
17D ARG* 1.3 74.1 + - + +
20D ARG* 2.6 79.5 + - + +
325D TRP* 3.9 24.9 - + + -
329D CYS* 3.1 34.2 + - + -
330D PHE* 3.5 39.9 - + - -
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Residues in contact with ARG 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLN 4.9 1.2 + - - -
13D GLN* 2.9 39.8 + - - +
14D GLN* 3.1 34.4 + - - +
16D TYR* 1.3 84.0 - - + +
18D GLU* 1.3 62.3 + - + +
20D ARG* 4.8 2.5 + - - +
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLN* 2.8 47.9 + - - +
15D TRP* 5.0 0.8 - - - -
17D ARG* 1.3 81.9 - - + +
19D HIS* 1.3 88.8 + - + +
20D ARG 3.8 0.2 - - - -
21D SER* 5.0 3.6 + - - -
22D GLU* 5.3 0.7 - - - -
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Residues in contact with HIS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TRP* 2.8 68.4 + + + +
18D GLU* 1.3 100.9 - - + +
20D ARG* 1.3 67.1 + - - +
21D SER* 3.1 4.5 - - - -
22D GLU* 2.8 53.2 + - - +
23D LEU* 3.6 5.5 + - - +
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Residues in contact with ARG 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D TYR* 2.6 68.2 + - + +
17D ARG* 4.8 2.4 + - - +
18D GLU 3.8 0.8 - - - -
19D HIS* 1.3 75.0 - - - +
21D SER* 1.3 63.0 + - - +
23D LEU* 3.0 33.4 + - - +
330D PHE* 3.8 31.9 + - + -
400D MET* 5.2 4.4 - - - -
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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