Contacts of the helix formed by residues 10 - 25 (chain S) in PDB entry 3H1J
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 GLY 10 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11S ARG* 1.3 53.8 + - - -
12S LEU* 2.6 24.0 + - - +
13S MET* 3.7 29.7 + - - +
14S ASP* 4.0 4.6 + - - +
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Residues in contact with ARG 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S GLY* 1.3 67.2 - - - -
12S LEU* 1.3 61.9 + - - +
14S ASP* 3.6 23.6 - - + +
15S ARG* 3.5 27.2 + - + +
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Residues in contact with LEU 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S GLY* 2.6 15.2 + - - +
11S ARG* 1.3 70.6 - - - +
13S MET* 1.3 73.1 + - + +
14S ASP 2.9 3.6 - - - -
15S ARG* 2.8 50.1 + - - +
16S ILE* 2.9 30.4 + - + +
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Residues in contact with MET 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S GLY 3.9 25.6 - - - +
12S LEU* 1.3 90.9 - - + +
14S ASP* 1.3 55.4 + - - +
15S ARG 3.2 0.2 - - - -
16S ILE* 3.2 25.1 - - + -
17S ARG* 2.5 61.4 + - + +
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Residues in contact with ASP 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S GLY 4.2 2.5 - - - +
11S ARG* 3.6 32.9 - - + +
12S LEU 2.9 0.2 - - - -
13S MET* 1.3 83.0 - - - +
15S ARG* 1.3 57.3 + - - +
17S ARG* 3.9 12.0 - - - +
18S LYS* 3.7 14.6 + - - +
83S TYR* 4.1 12.9 + - - -
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Residues in contact with ARG 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S ARG* 3.5 22.5 + - + +
12S LEU* 2.8 42.0 + - - +
14S ASP* 1.3 77.0 - - - +
16S ILE* 1.3 68.2 + - + +
17S ARG 3.2 1.6 - - - -
18S LYS* 3.2 10.8 + - + +
19S TRP* 2.9 22.2 + - - +
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Residues in contact with ILE 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377P MET* 3.8 32.1 - - + -
12S LEU* 2.9 36.2 + - + +
13S MET* 3.2 28.5 - - + +
15S ARG* 1.3 78.5 - - + +
17S ARG* 1.3 66.9 + - + +
19S TRP* 2.8 22.6 + - + +
20S TYR* 2.9 12.1 + - - +
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Residues in contact with ARG 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376P LYS* 3.5 18.2 + - - +
377P MET* 3.5 24.3 - - - +
379P ASN* 2.9 46.7 + - - +
13S MET* 2.5 62.4 + - + +
14S ASP* 3.9 7.8 - - - +
16S ILE* 1.3 75.9 - - + +
18S LYS* 1.3 57.3 + - - +
20S TYR* 3.1 3.9 + - - +
21S TYR* 2.8 30.5 + - - +
83S TYR* 3.5 25.3 - - + +
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Residues in contact with LYS 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ASP 3.7 6.7 + - - +
15S ARG* 3.2 14.3 + - + +
17S ARG* 1.3 78.3 - - - +
19S TRP* 1.3 58.5 + - - +
21S TYR* 3.5 1.6 + - - +
22S ASN* 2.4 44.1 + - - +
83S TYR* 3.5 40.5 - - + +
84S GLU* 2.7 39.1 + - - +
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Residues in contact with TRP 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320P PRO* 5.2 3.1 - - + -
321P LEU* 4.3 21.3 - - + -
377P MET* 3.5 28.3 - - + -
15S ARG 2.9 11.5 + - - +
16S ILE* 2.8 18.4 + - + +
18S LYS* 1.3 78.2 - - - +
20S TYR* 1.3 79.4 + + - +
22S ASN* 3.0 10.6 + - + +
23S ALA* 2.8 45.8 + - + +
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Residues in contact with TYR 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313P GLN* 4.7 1.4 + - - -
318P PHE 3.7 13.7 + - - -
319P ARG* 3.7 5.0 - - - +
320P PRO* 3.7 25.1 - - + -
321P LEU* 4.4 4.0 - - + -
374P GLU* 2.9 47.3 + - + +
377P MET* 3.4 47.8 - - + -
378P LEU* 3.5 39.4 - - + +
16S ILE 2.9 7.3 + - - +
17S ARG* 3.5 7.6 - - - +
19S TRP* 1.3 87.8 - + - +
21S TYR* 1.3 56.7 + - - +
23S ALA* 2.9 2.7 + - - +
24S ALA* 2.6 39.9 + - + +
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Residues in contact with TYR 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378P LEU* 5.6 3.6 - - + -
17S ARG 2.8 20.5 + - - +
18S LYS 3.6 3.4 - - - +
20S TYR* 1.3 77.6 - - - +
22S ASN* 1.3 68.1 + - - +
24S ALA* 3.9 6.2 + - - +
25S GLY 3.6 12.5 + - - -
26S PHE* 3.7 29.3 - + - -
27S ASN* 3.6 28.6 - - + +
31S LEU 4.3 0.5 + - - -
33S ARG* 5.1 3.6 - - + -
81S VAL* 3.3 35.5 - - - +
83S TYR* 3.5 47.6 - + + -
86S ASP* 3.0 37.2 + - + -
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Residues in contact with ASN 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S LYS* 2.4 43.6 + - - +
19S TRP* 3.0 8.8 + - + +
21S TYR* 1.3 88.0 - - - +
23S ALA* 1.3 66.1 + - - +
25S GLY 3.5 6.8 + - - +
27S ASN* 4.6 11.3 + - - +
28S LYS* 3.5 18.7 + - - +
83S TYR* 4.9 4.3 + - - +
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Residues in contact with ALA 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320P PRO* 4.0 22.6 - - + +
19S TRP* 2.8 34.2 + - + +
20S TYR* 3.3 12.8 - - - +
22S ASN* 1.3 76.9 - - - +
24S ALA* 1.3 68.0 + - - +
25S GLY* 3.2 1.2 + - - -
28S LYS* 5.4 0.3 + - - -
47T LYS* 4.5 14.2 + - - -
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Residues in contact with ALA 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317P THR 4.0 3.8 - - - +
318P PHE* 3.2 46.2 - - - +
320P PRO* 4.1 5.2 - - - +
323P GLN* 5.6 0.3 + - - -
378P LEU* 5.2 0.2 - - + -
20S TYR* 2.6 29.5 + - + +
21S TYR 4.0 2.2 - - - +
23S ALA* 1.3 74.1 - - - +
25S GLY* 1.3 62.5 + - - +
26S PHE* 3.4 30.2 + - + -
47T LYS* 5.7 0.5 + - - -
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Residues in contact with GLY 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318P PHE* 4.4 2.9 - - - -
21S TYR 3.6 4.6 + - - -
22S ASN 3.5 3.9 + - - -
23S ALA 3.2 3.5 - - - -
24S ALA* 1.3 79.4 - - - +
26S PHE* 1.3 56.0 + - - +
27S ASN* 2.9 16.2 - - - -
28S LYS* 2.8 49.2 + - - +
29S TYR* 4.2 4.9 + - - -
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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