Contacts of the strand formed by residues 107 - 116 (chain B) in PDB entry 3QR2
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 VAL 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 4.7 1.8 - - - +
110A GLN* 3.1 41.3 - - + +
111A ALA* 4.4 4.9 - - - +
112A VAL* 4.9 12.3 - - + +
2B ALA* 3.8 27.4 - - + +
3B GLY* 4.4 1.3 - - - -
4B PHE* 3.2 21.0 - - + -
88B ARG* 3.3 4.2 - - - -
89B ALA* 3.0 56.7 + - + +
105B LYS 4.1 0.8 + - - -
106B TRP* 1.3 71.1 - - - +
108B ARG* 1.3 60.0 + - - +
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 5.9 0.2 - - - -
108A ARG* 4.0 4.2 - - + +
109A ALA* 3.4 2.4 - - - -
110A GLN* 2.8 57.6 + - - +
4B PHE* 3.3 6.2 - - - -
46B CYS* 6.0 0.6 - - - +
86B GLU* 3.4 30.9 + - - +
87B CYS 3.5 3.4 - - - -
88B ARG* 3.2 45.2 - - + +
105B LYS* 6.4 0.2 - - - +
106B TRP* 3.4 21.6 + - - +
107B VAL* 1.3 75.3 - - - +
109B ALA* 1.3 58.5 + - - +
110B GLN* 5.3 1.3 - - + -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 5.4 0.2 - - + -
108A ARG 3.5 5.2 - - - -
109A ALA* 4.1 6.5 - - + +
4B PHE* 3.6 29.8 - - + -
7B ALA* 4.0 12.6 - - + -
8B PRO* 3.5 25.5 - - + +
86B GLU* 4.4 0.4 - - - +
87B CYS 3.0 30.1 + - - -
108B ARG* 1.3 74.2 - - - +
110B GLN* 1.3 63.4 + - - +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE* 3.6 23.3 + - - -
106A TRP 3.6 7.1 - - - +
107A VAL* 3.8 8.9 - - + +
108A ARG* 2.8 60.6 + - + +
8B PRO* 3.9 7.7 - - - +
10B SER* 4.9 0.3 + - - -
84B THR* 3.9 23.4 - - + +
85B TYR 3.5 5.8 - - - +
86B GLU* 3.1 34.7 + - + +
108B ARG* 5.3 0.7 - - + -
109B ALA* 1.3 78.6 - - - +
111B ALA* 1.3 61.7 + - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 4.4 2.5 - - - -
8B PRO* 3.6 22.4 - - + +
9B LEU 3.5 9.4 - - - +
10B SER* 3.5 28.0 - - - +
21B LEU* 4.4 10.5 - - + -
84B THR* 3.6 2.6 - - - -
85B TYR* 2.8 35.3 + - - +
110B GLN* 1.3 74.1 - - - +
112B VAL* 1.3 64.5 + - - +
113B VAL* 5.2 0.2 - - - -
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.0 24.6 - - + +
2A ALA 5.0 2.0 - - - +
107A VAL* 3.9 18.1 - - + +
10B SER* 2.9 18.8 + - - +
11B GLN 2.8 25.6 + - - +
40B GLN* 5.5 5.8 - - - +
82B THR* 6.1 0.4 - - + -
83B GLY* 3.5 8.1 - - - +
84B THR* 3.7 22.9 - - - +
111B ALA* 1.3 74.8 - - - +
113B VAL* 1.3 70.5 + - - +
114B LEU* 4.4 2.9 - - + +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLN 3.2 10.5 - - - +
13B ARG* 5.6 1.1 - - + -
19B VAL* 4.3 27.6 - - + -
21B LEU* 3.8 28.7 - - + -
77B LEU* 5.0 2.9 - - + -
81B ASP 4.5 2.5 - - - +
82B THR* 3.1 6.1 - - - +
83B GLY 2.8 36.6 + - - -
85B TYR* 3.7 34.1 - - + +
112B VAL* 1.3 80.6 - - - +
114B LEU* 1.3 61.5 + - - +
115B VAL* 4.3 18.2 - - + -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.7 23.8 - - + +
11B GLN 3.0 7.9 + - - +
12B GLN* 3.3 12.0 - - + +
13B ARG 2.8 27.5 + - - +
40B GLN* 5.4 2.5 - - - +
82B THR* 3.8 19.1 - - + +
112B VAL* 4.9 3.1 - - + -
113B VAL* 1.3 72.4 - - - +
115B VAL* 1.3 64.8 + - - +
116B LEU* 3.7 34.1 - - + -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG 3.4 3.1 - - - +
14B TRP 3.9 4.5 - - - -
15B VAL* 3.6 37.5 - - + +
77B LEU* 3.7 26.5 - - + -
78B VAL 3.6 28.7 - - - +
79B GLU* 3.8 13.9 - - - +
81B ASP* 4.2 5.6 - - + -
82B THR* 2.9 30.2 + - - +
113B VAL* 4.3 9.0 - - + -
114B LEU* 1.3 78.1 - - - +
116B LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLN* 3.4 35.0 - - + +
13B ARG 2.9 8.2 + - - +
14B TRP* 3.5 25.0 - - + -
15B VAL* 3.1 18.7 + - - -
79B GLU* 5.3 0.2 - - - -
114B LEU* 3.7 36.6 - - + -
115B VAL* 1.3 74.9 - - - +
117B GLU* 1.3 67.4 - - - +
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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