Contacts of the helix formed by residues 28 - 35 (chain A) in PDB entry 4H3T
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 SER 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU 4.1 0.9 - - - -
10A SER 3.4 17.2 + - - -
11A SER* 3.5 16.9 + - - -
12A GLU 3.3 23.9 + - - -
13A PRO* 4.0 1.6 - - - +
14A TRP* 4.4 0.9 - - - -
15A LEU* 4.1 2.7 - - - -
27A VAL* 1.3 75.9 - - - +
29A LEU* 1.3 59.5 + - - +
30A ARG* 4.0 1.4 - - - +
31A ASP* 3.1 29.0 + - - +
32A ILE* 2.9 27.9 + - - +
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Residues in contact with LEU 29 (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 LEU* 3.1 23.7 + - + +
10A SER* 4.1 2.2 - - - +
14A TRP* 3.9 21.8 - - + -
15A LEU* 3.5 19.2 - - + +
28A SER* 1.3 70.3 - - - +
30A ARG* 1.3 65.9 + - - +
32A ILE* 3.3 10.3 - - + +
33A PHE* 3.3 22.2 - - - -
56A LEU* 4.6 8.1 - - + -
57A VAL* 4.3 14.8 - - + -
60A LEU* 3.7 21.3 - - + -
92A PHE* 3.8 17.0 - - + -
99A PHE* 3.7 36.1 - - + -
108A PHE* 5.7 0.9 - - + -
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Residues in contact with ARG 30 (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 SER 3.1 21.8 + - - +
11A SER* 5.3 0.9 - - - -
28A SER* 4.0 1.8 - - - +
29A LEU* 1.3 78.9 - - - +
31A ASP* 1.3 76.0 + - - +
33A PHE* 3.2 3.3 + - - +
34A VAL* 3.0 48.6 + - - +
85A GLU* 2.9 27.7 + - - -
88A ILE* 3.9 10.9 - - + +
89A ASP* 2.8 40.9 + - - +
92A PHE* 3.9 19.4 - - + -
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Residues in contact with ASP 31 (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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27A VAL* 4.0 18.0 - - + +
28A SER* 3.1 21.0 + - - +
30A ARG* 1.3 96.9 + - - +
32A ILE* 1.3 61.4 + - - +
34A VAL* 4.3 5.1 - - - +
35A LEU* 2.8 52.6 + - + +
39A ILE* 4.4 0.3 - - - +
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Residues in contact with ILE 32 (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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15A LEU* 4.0 17.9 - - + -
17A VAL* 4.1 13.2 - - + -
27A VAL* 3.8 15.0 - - + +
28A SER 2.9 15.9 + - - +
29A LEU* 3.3 20.9 - - - +
31A ASP* 1.3 76.3 - - - +
33A PHE* 1.3 70.0 + - + +
36A ALA* 3.2 27.4 + - - +
39A ILE* 4.3 4.7 - - + +
42A PHE* 3.7 33.7 - - + -
57A VAL* 4.4 13.7 - - + -
207A LEU* 3.6 24.2 - - + +
211A LEU* 5.3 1.3 - - - +
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Residues in contact with PHE 33 (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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29A LEU* 3.3 19.3 - - + -
30A ARG 3.2 6.5 + - - +
32A ILE* 1.3 81.1 - - + +
34A VAL* 1.3 66.9 + - - +
35A LEU 3.2 1.6 + - - -
36A ALA* 3.3 9.4 + - - +
37A HIS* 5.2 0.3 + - - -
57A VAL* 3.3 41.5 - - + -
60A LEU* 3.8 23.1 - - + -
61A ALA* 3.7 30.1 - - + -
64A ILE* 4.0 18.6 - - + -
65A LEU* 6.0 1.8 - - + -
83A PHE* 3.5 39.7 + + + +
88A ILE* 3.5 24.2 - - + -
92A PHE* 4.8 1.8 - + - -
211A LEU* 4.2 13.5 - - + -
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Residues in contact with VAL 34 (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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30A ARG* 3.0 51.5 + - - +
31A ASP* 4.3 5.6 - - - +
33A PHE* 1.3 76.5 - - - +
35A LEU* 1.3 70.8 + - + +
37A HIS* 3.3 20.8 + - - -
82A ARG* 5.0 3.3 - - - +
83A PHE 5.0 5.2 + - - +
85A GLU* 3.7 35.0 - - + +
88A ILE* 3.6 24.5 - - + -
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Residues in contact with LEU 35 (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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19A PHE* 4.2 22.2 - - + -
23A ARG* 6.1 0.4 - - - +
27A VAL* 5.1 2.5 - - + -
31A ASP* 2.8 44.1 + - + +
34A VAL* 1.3 90.5 - - + +
36A ALA* 1.4 57.0 + - - +
37A HIS* 3.2 7.9 - - + -
38A THR* 2.8 47.4 + - + +
39A ILE* 3.4 14.6 - - + +
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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