Contacts of the strand formed by residues 109 - 117 (chain B) in PDB entry 2Q7V
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 GLU 109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B HIS* 2.9 27.5 - - - +
102B THR* 4.9 14.7 + - - +
103B VAL 3.3 4.5 - - - +
104B ARG* 3.7 37.1 - - + +
105B GLY 5.8 0.4 - - - +
108B GLY* 1.3 74.3 - - - +
110B TYR* 1.3 64.0 + - - +
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Residues in contact with TYR 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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7B HIS* 3.3 46.5 + + + +
9B TYR* 3.9 9.2 - + + -
12B VAL* 4.3 18.6 - - + -
35B LEU* 3.5 23.3 - - + -
37B LEU* 3.8 30.1 - - + +
83B GLU* 2.8 33.6 + - - -
85B ASP* 4.9 5.5 + - - -
102B THR* 3.2 5.5 - - - -
103B VAL* 2.7 51.0 + - + +
105B GLY 5.1 1.8 - - - -
107B ASN 5.5 0.2 - - - -
108B GLY* 3.7 24.9 + - - -
109B GLU* 1.3 77.5 - - - +
111B ARG* 1.3 64.2 + - - +
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Residues in contact with ARG 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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7B HIS* 2.8 8.6 + - + +
8B ASP* 2.9 39.4 + - - +
9B TYR* 2.8 28.8 + - - +
12B VAL* 4.4 0.3 - - - +
96B SER* 4.8 8.1 + - - -
97B HIS 5.3 1.8 + - - -
98B PRO* 5.1 4.2 - - - +
99B TYR* 3.4 46.2 + - + +
101B PHE 3.3 9.9 - - - +
102B THR* 4.6 12.1 - - + +
110B TYR* 1.3 76.8 - - - +
112B ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 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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9B TYR 3.1 7.4 - - - +
12B VAL* 3.5 26.9 - - + +
99B TYR* 3.4 12.5 - - - -
100B PRO* 3.5 0.2 - - - +
101B PHE* 3.0 32.8 + - + +
103B VAL* 4.8 1.8 - - + -
110B TYR 4.1 0.2 + - - -
111B ARG* 1.3 74.4 - - - +
113B LYS* 1.3 61.1 + - - +
114B ALA 3.4 22.0 - - - +
115B VAL* 4.0 11.9 - - + -
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Residues in contact with LYS 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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9B TYR 3.2 6.7 + - - +
10B ASP* 3.3 35.8 + - - +
98B PRO* 3.3 39.6 - - + +
99B TYR* 3.7 31.6 + - + -
100B PRO* 3.8 7.3 - - - +
101B PHE* 3.6 13.0 - - - -
112B ALA* 1.3 73.6 - - - +
114B ALA* 1.3 60.0 + - - +
278B MET* 3.8 11.8 - - - +
311B LEU* 3.7 25.8 - - + +
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Residues in contact with ALA 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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10B ASP 3.0 9.1 + - - +
11B VAL* 3.3 5.5 - - + -
12B VAL 3.0 24.1 + - - -
101B PHE* 3.9 1.6 - - - -
112B ALA* 3.3 5.4 - - - +
113B LYS* 1.3 80.3 - - - +
115B VAL* 1.3 65.2 + - - +
278B MET* 3.4 25.1 - - + +
307B THR* 3.6 33.9 - - + +
311B LEU* 4.5 1.8 - - + -
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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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12B VAL 3.2 11.0 - - - +
14B ILE* 3.8 26.9 - - + -
90B VAL* 4.6 3.8 - - + -
101B PHE* 3.4 36.7 - - + -
103B VAL* 3.9 16.6 - - + -
112B ALA* 4.0 3.4 - - + -
114B ALA* 1.3 77.6 - - - +
116B ILE* 1.3 70.7 + - - +
117B LEU* 4.4 1.8 - - + +
278B MET 3.0 7.4 + - - +
279B LEU* 3.2 27.8 - - + -
280B PHE* 2.9 25.8 + - - +
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Residues in contact with ILE 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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11B VAL* 3.8 20.0 - - + -
12B VAL 3.0 7.9 + - - +
13B ILE* 3.4 11.5 - - + +
14B ILE* 2.9 28.2 + - - +
23B ALA* 3.9 28.5 - - + -
27B THR* 4.4 3.6 - - - +
115B VAL* 1.3 78.9 - - - +
117B LEU* 1.3 64.7 + - - +
118B ALA* 3.5 6.0 + - + -
280B PHE* 3.4 8.3 - - + +
282B ALA* 4.3 15.0 - - + -
303B ALA* 3.9 21.8 - - + -
304B ALA* 4.2 15.5 - - - +
307B THR* 3.8 24.7 - - - +
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Residues in contact with LEU 117 (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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14B ILE* 4.2 9.4 - - + +
115B VAL* 4.0 4.6 - - + +
116B ILE* 1.3 71.6 - - - +
118B ALA* 1.3 60.4 + - - +
119B THR* 3.1 37.9 - - + +
250B ASN 4.5 0.2 - - - +
251B THR* 4.7 1.3 - - + -
253B PHE* 4.2 14.4 - - + -
254B VAL* 4.2 23.8 - - + -
258B VAL* 5.1 2.7 - - + -
266B VAL* 3.8 29.8 - - + -
279B LEU* 4.5 14.8 - - + -
280B PHE 2.7 17.1 + - - +
281B ALA* 3.3 5.3 - - + -
282B ALA 3.0 23.1 + - - -
285B VAL* 3.5 10.4 - - + +
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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