Contacts of the strand formed by residues 33 - 39 (chain J) in PDB entry 2VLR
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 33 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J HIS* 3.5 0.7 - - - +
32J ASP* 1.3 76.6 - - - +
34J MET* 1.3 65.9 + - - +
35J TYR* 3.8 9.2 - - - +
51J SER 3.2 10.1 - - - +
52J GLN 3.9 5.4 - - - +
95J SER* 3.2 6.9 - - - -
96J SER* 3.1 40.6 + - - +
99J ALA* 3.6 34.8 - - + +
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Residues in contact with MET 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J CYS* 5.0 9.6 - - - +
27J GLN* 3.9 22.7 - - - +
31J HIS 5.4 0.2 - - - +
33J ALA* 1.3 77.6 - - - +
35J TYR* 1.3 64.5 + - - +
50J TYR* 3.3 4.7 - - - +
51J SER* 2.8 38.8 + - - +
70J ARG* 2.6 39.6 - - - +
73J LYS 2.6 31.0 - - - +
74J GLU 4.4 1.3 - - - +
75J SER 3.5 20.6 - - - +
76J PHE* 3.6 31.7 - - + -
93J CYS* 5.1 1.6 - - - -
94J ALA 3.3 8.5 - - - +
95J SER* 4.1 10.3 - - - -
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Residues in contact with TYR 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I GLY 2.7 22.9 + - - -
98I ASN* 3.9 10.5 - - + -
33J ALA* 3.8 15.9 - - + +
34J MET* 1.3 76.4 - - - +
36J TRP* 1.3 59.9 + - - +
37J TYR* 3.8 23.6 - - + -
47J LEU* 4.3 11.2 - - + -
49J TYR 3.8 4.5 - - - -
50J TYR* 3.4 37.1 - + + -
51J SER 5.1 0.8 + - - -
52J GLN* 5.4 0.2 - - - +
76J PHE* 4.0 2.2 - - - -
92J LEU 4.7 0.4 - - - -
93J CYS* 3.3 11.3 - - - -
94J ALA* 2.9 35.6 + - + +
95J SER* 4.6 0.2 - - - -
96J SER* 3.5 19.5 - - - -
99J ALA* 3.4 20.4 - - - +
100J SER 3.7 3.5 + - - -
103J GLN* 3.6 30.7 - - + +
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Residues in contact with TRP 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J GLN* 3.3 31.2 - - - -
23J LEU* 3.9 29.4 - - + -
24J SER 4.0 7.6 - - - -
25J CYS* 3.6 18.8 - - + -
35J TYR* 1.3 71.8 - - - +
37J TYR* 1.3 64.4 + - - +
47J LEU* 3.6 8.8 - - - +
48J ILE* 3.0 35.5 + - + +
49J TYR* 3.1 14.2 + - + +
68J VAL* 4.4 7.2 - - + -
76J PHE* 2.8 51.4 + + - -
78J LEU* 3.5 37.3 - - + +
91J TYR* 3.9 19.3 - - + -
92J LEU 3.6 22.7 - - - -
93J CYS* 4.0 13.3 - - + -
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Residues in contact with TYR 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I ASN* 6.1 0.2 - - - +
99I LEU* 4.9 4.6 + - - +
101I PHE* 3.6 28.9 - + - -
35J TYR* 3.8 21.7 - - + +
36J TRP* 1.3 76.5 - - - +
38J ARG* 1.3 60.4 + - - +
45J LEU* 4.0 27.8 - - + -
46J ARG 3.2 8.7 - - - +
47J LEU* 3.9 33.3 - - + +
48J ILE* 3.8 5.3 - - - +
91J TYR* 3.7 8.1 - - - +
92J LEU* 2.9 43.8 + - + +
94J ALA* 4.2 2.7 - - + -
103J GLN* 2.6 40.2 + - - -
105J PHE* 3.7 24.7 - + - -
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Residues in contact with ARG 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J TYR* 1.3 76.3 - - - +
39J GLN* 1.3 62.6 + - - +
40J ASP* 2.9 31.1 + - - -
44J GLY 4.0 0.5 - - - +
45J LEU* 3.8 2.6 - - - -
46J ARG* 2.9 64.5 + - + +
48J ILE* 3.8 15.9 - - + +
62J ILE* 4.6 15.9 - - + +
66J TYR* 3.1 29.1 + - - -
84J GLN 5.5 0.6 + - - -
86J ASN* 3.0 38.7 + - - +
88J THR 3.6 9.7 + - - -
89J ALA* 3.8 10.5 - - + +
90J PHE 3.4 7.0 - - - +
91J TYR* 3.8 12.7 + - + -
92J LEU* 6.3 0.2 - - - -
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Residues in contact with GLN 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I GLN* 3.1 39.4 + - - -
41I GLY 5.7 0.9 + - - -
87I LEU* 4.3 6.5 - - - +
89I LEU* 6.2 0.2 - - - +
38J ARG* 1.3 77.6 - - - +
40J ASP* 1.3 74.5 + - - +
41J PRO* 4.7 0.9 - - - +
42J GLY 6.0 0.2 - - - +
43J GLN 2.8 23.7 + - - +
44J GLY* 3.5 18.6 - - - +
45J LEU* 4.3 15.2 - - + +
89J ALA* 4.2 1.6 - - - +
90J PHE* 2.8 57.3 + - + +
92J LEU* 4.2 2.3 - - + +
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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