Contacts of the strand formed by residues 35 - 40 (chain A) in PDB entry 5HS6
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 ARG 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLY* 4.3 19.4 + - - +
10A LYS 2.9 10.3 + - - +
11A VAL* 3.4 29.6 - - + +
12A VAL* 2.9 26.3 + - - +
33A GLY 3.9 1.0 + - - +
34A ALA* 1.3 75.2 - - - +
36A VAL* 1.3 61.1 + - - +
37A VAL* 5.9 0.4 - - - -
55A GLY* 3.3 18.6 - - - +
79A ARG 5.3 0.4 + - - -
80A PHE* 3.9 50.1 + - + +
82A ARG* 5.0 4.0 - - - +
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Residues in contact with VAL 36 (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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12A VAL* 3.2 10.8 - - + +
14A VAL* 4.0 11.2 - - + -
26A VAL* 3.9 31.0 - - + +
29A PHE* 3.6 30.7 - - + -
30A VAL* 3.7 27.6 - - + +
34A ALA 4.2 2.0 - - - +
35A ARG* 1.3 79.4 - - - +
37A VAL* 1.3 76.5 + - - +
38A ILE* 3.8 1.1 + - + +
55A GLY 2.9 7.7 + - - +
56A ALA* 3.2 4.0 - - + -
57A VAL* 3.0 27.9 + - - +
80A PHE* 5.5 2.0 - - - -
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Residues in contact with VAL 37 (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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11A VAL* 4.8 2.7 - - + -
12A VAL 2.7 14.3 + - - +
13A VAL* 3.6 8.1 - - + +
14A VAL 3.1 25.5 + - - -
36A VAL* 1.3 74.8 - - - +
38A ILE* 1.3 63.6 + - - +
39A CYS 3.5 0.7 + - - -
57A VAL* 3.5 6.3 - - + +
59A ILE* 3.8 33.0 - - + -
72A LEU* 3.8 21.3 - - + -
76A THR* 3.6 21.8 - - + +
80A PHE* 3.6 34.1 - - + -
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Residues in contact with ILE 38 (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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14A VAL 3.9 2.5 - - - -
17A GLY* 3.5 35.9 - - - +
18A GLY 3.9 2.9 - - - +
26A VAL* 3.9 22.4 - - + -
36A VAL* 4.5 0.7 - - + -
37A VAL* 1.3 72.9 - - - +
39A CYS* 1.3 60.3 + - - +
46A GLY* 4.0 7.6 - - - +
49A LEU* 3.7 30.3 - - + -
50A GLU 3.9 9.2 - - - +
56A ALA* 3.7 25.1 - - + -
57A VAL 2.6 19.5 + - - +
58A PHE* 3.4 18.1 - - + -
59A ILE* 2.7 32.6 + - - +
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Residues in contact with CYS 39 (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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13A VAL* 4.6 2.7 - - + -
14A VAL 2.9 15.2 + - - +
15A THR* 3.8 25.4 - - + -
16A GLY 2.8 24.2 + - - -
17A GLY 3.0 8.8 + - - -
37A VAL 3.5 0.8 + - - -
38A ILE* 1.3 72.4 - - - +
40A ASP* 1.3 65.8 + - - +
59A ILE 3.5 5.6 - - - +
61A CYS* 3.6 27.8 - - - -
63A VAL* 4.0 8.5 - - - -
72A LEU* 3.9 28.9 - - + -
301A NAD 4.5 0.7 - - - -
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Residues in contact with ASP 40 (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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16A GLY* 3.2 8.7 - - - -
18A GLY* 2.9 24.9 + - - +
39A CYS* 1.3 75.1 - - - +
41A LYS* 1.3 72.9 + - - +
42A ASP* 3.0 18.3 + - - +
58A PHE* 3.6 19.4 - - + -
59A ILE 3.6 4.4 + - - -
60A LEU* 3.5 10.0 - - - +
61A CYS 2.9 24.2 + - - -
301A NAD 2.6 55.4 + - - -
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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