Contacts of the strand formed by residues 86 - 94 (chain D) in PDB entry 3VXR
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 ALA 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D ARG* 3.6 32.8 - - + +
38D GLN 3.4 13.5 - - - +
39D ASP* 3.8 4.5 - - - +
40D PRO* 5.6 4.0 - - - -
84D ASP 3.1 8.8 + - - +
85D SER* 1.3 76.4 - - - +
87D THR* 1.3 61.9 + - - +
88D TYR* 3.5 10.3 - - + -
107D ARG* 4.9 1.6 - - - -
108D LEU* 2.8 32.2 + - - -
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Residues in contact with THR 87 (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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37D ARG* 3.5 3.3 - - - -
38D GLN* 2.8 55.7 + - - +
40D PRO* 5.9 1.8 - - - +
86D ALA* 1.3 72.5 - - - +
88D TYR* 1.3 65.2 + - - +
89D LEU* 3.9 9.9 + - + -
104D SER 4.7 4.5 - - - +
105D GLY* 4.3 17.7 - - - -
106D THR 3.5 12.6 - - - +
107D ARG* 4.3 17.0 - - + +
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLN* 2.8 25.4 + - - -
21D LEU* 4.8 11.2 - - + -
35D TRP* 4.4 12.1 - + + -
36D PHE 3.4 4.3 - - - +
37D ARG* 3.7 16.6 + - + -
47D LEU* 3.7 32.5 - - + -
62D LEU* 5.3 5.3 - - + +
75D LEU* 4.0 13.9 - - + -
77D ILE* 4.2 17.9 - - + +
84D ASP* 2.6 44.4 + - - +
86D ALA* 3.5 24.7 - - + -
87D THR* 1.3 71.7 - - - +
89D LEU* 1.3 57.4 + - - +
105D GLY* 3.1 1.3 - - - -
106D THR* 2.9 29.6 + - - +
108D LEU* 3.7 20.4 - - + -
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Residues in contact with LEU 89 (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 GLN* 3.7 0.7 - - - -
34D GLN 3.7 1.0 - - - +
35D TRP* 3.4 9.5 - - - -
36D PHE* 2.8 49.1 + - + +
38D GLN* 3.5 32.8 - - + +
44D LEU* 3.9 28.5 - - + -
87D THR* 4.6 7.4 - - + +
88D TYR* 1.3 73.9 - - - +
90D CYS* 1.3 60.7 + - - +
102D PHE* 4.1 10.1 - - + -
103D GLY 3.8 22.7 - - - +
104D SER 4.1 5.4 - - - +
105D GLY* 4.0 15.0 - - - +
37E GLN* 4.7 2.7 - - - +
42E GLY* 4.4 2.2 - - - -
43E PRO* 4.0 17.9 - - + -
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Residues in contact with CYS 90 (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 VAL* 4.1 3.3 - - + +
6D GLN* 2.9 23.4 + - + +
23D CYS* 2.0 52.3 - - + -
33D LEU* 4.1 23.8 - - - -
34D GLN 3.8 2.9 - - - -
35D TRP* 3.8 8.7 - - + -
89D LEU* 1.3 74.1 - - - +
91D ALA* 1.3 63.9 + - - +
92D VAL* 4.8 0.7 - - - -
101D ILE 4.0 0.2 - - - +
102D PHE* 3.5 3.2 - - - -
103D GLY 2.8 29.3 + - - -
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Residues in contact with ALA 91 (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 VAL* 5.5 0.2 - - - -
33D LEU* 3.3 5.5 - - - +
34D GLN 2.8 42.5 + - - +
36D PHE* 4.0 3.6 - - + -
90D CYS* 1.3 76.0 - - - +
92D VAL* 1.3 63.9 + - - +
100D LEU* 3.8 22.6 - - + +
101D ILE 3.3 9.0 - - - +
102D PHE* 3.7 29.6 - - + -
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Residues in contact with VAL 92 (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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2D GLN* 3.9 7.2 - - - +
4D VAL* 3.8 25.4 - - + -
25D PHE* 4.0 18.8 - - + -
30D ILE* 3.9 10.3 - - + -
32D ASN 3.6 5.6 - - - +
33D LEU* 3.7 25.6 - - + -
90D CYS* 4.8 4.5 - - - -
91D ALA* 1.3 79.7 - - - +
93D ARG* 1.3 60.0 + - - +
94D MET* 3.2 25.6 - - + -
100D LEU* 3.5 5.1 - - - -
101D ILE* 2.8 43.4 + - + +
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Residues in contact with ARG 93 (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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4C LEU* 3.8 9.9 - - - -
6C PHE* 3.5 28.1 - - - -
30D ILE* 3.5 8.8 - - - +
31D TYR* 2.7 31.7 + - + -
32D ASN* 2.7 56.4 + - - +
92D VAL* 1.3 74.4 - - - +
94D MET* 1.3 58.4 + - - +
97D SER 3.2 23.3 - - - +
98D TYR 2.8 15.7 + - - -
99D LYS 3.7 9.0 - - - +
100D LEU* 3.8 15.9 - - + +
33E TYR* 3.2 17.2 + - - -
99E THR 4.6 0.6 + - - -
100E GLY* 2.9 36.7 + - - -
102E LEU* 3.1 21.4 - - - +
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Residues in contact with MET 94 (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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4C LEU* 3.7 3.6 - - - +
2D GLN* 3.4 28.0 - - + +
27D ASP* 4.8 10.8 - - - +
29D ALA 3.6 8.7 - - - +
30D ILE* 3.1 33.0 - - + -
31D TYR* 3.9 1.8 - - - -
92D VAL* 3.2 25.8 - - + +
93D ARG* 1.3 78.5 - - - +
95D ASP* 1.3 62.7 + - - +
96D SER* 2.9 22.4 - - - +
97D SER* 2.9 32.7 + - - +
99D LYS* 4.6 2.2 + - - -
101D ILE* 3.9 20.6 - - + -
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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