Contacts of the strand formed by residues 68 - 75 (chain B) in PDB entry 1VQ7
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 THR 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27190 A 5.7 4.0 - - + -
50B HIS* 3.4 38.4 - - + -
51B VAL 5.0 0.7 - - - +
52B VAL* 4.2 15.6 - - + +
67B GLU* 1.3 75.8 - - - +
69B VAL* 1.3 68.2 + - - +
70B PRO* 4.3 3.6 - - - +
81K ARG* 5.3 6.1 + - - -
83K PRO 3.2 10.5 + - - +
84K ASP* 2.6 35.5 + - - +
85K GLY* 4.0 6.7 - - - -
16U GLY* 3.8 12.2 - - - +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 3.2 4.9 - - - -
51B VAL* 2.8 45.2 + - - +
53B LEU* 4.4 16.2 - - + -
67B GLU* 4.3 22.7 - - + +
68B THR* 1.3 81.1 - - - +
70B PRO* 1.3 83.6 - - + +
71B VAL* 4.3 7.6 - - + -
270B ILE* 4.7 7.9 - - + -
298B LYS* 3.9 30.1 - - + -
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Residues in contact with PRO 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27190 A 3.3 48.5 - - + +
27640 C 3.6 23.8 - - - +
27650 C 4.8 11.4 - - - +
48B MET* 4.3 9.0 - - + -
49B THR 4.0 4.0 - - - +
68B THR 4.3 3.8 - - - +
69B VAL* 1.3 93.9 - - + +
71B VAL* 1.3 66.4 + - - +
298B LYS* 3.8 0.8 - - + -
299B GLY* 2.9 25.8 + - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B MET* 3.1 9.0 - - - +
49B THR* 2.8 45.5 + - - +
50B HIS 5.3 0.2 - - - -
51B VAL* 3.3 31.2 - - + -
69B VAL* 4.0 2.0 - - + +
70B PRO* 1.3 80.3 - - - +
72B THR* 1.3 65.5 + - - +
73B VAL* 3.8 3.5 + - + +
270B ILE* 4.3 19.1 - - + -
296B LEU* 3.5 43.1 - - + -
297B VAL 3.3 11.0 - - - +
299B GLY 3.9 2.2 - - - -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27170 C 4.9 0.3 + - - -
45B LYS* 4.1 26.6 - - + -
47B GLY 3.2 11.2 - - - +
48B MET* 3.2 15.0 - - + +
71B VAL* 1.3 74.4 - - - +
73B VAL* 1.3 64.9 + - - +
74B ILE* 3.6 19.7 + - + +
297B VAL* 2.9 32.5 + - - +
299B GLY 2.7 21.1 + - - -
300B SER* 3.6 7.4 - - - -
301B VAL* 3.9 19.0 + - + -
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA* 3.1 25.5 + - + +
47B GLY 2.7 17.3 + - - +
49B THR* 3.9 18.2 - - - +
71B VAL* 4.4 2.2 - - + +
72B THR* 1.3 73.1 - - - +
74B ILE* 1.3 68.1 + - - +
278B PRO* 4.1 24.7 - - + -
284B PHE* 3.8 35.0 - - + -
290B VAL* 4.4 10.5 - - + -
294B TYR* 4.8 6.1 - - + -
295B THR 3.8 4.9 - - - +
296B LEU* 3.7 20.4 - - + -
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Residues in contact with ILE 74 (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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44B TYR 3.7 25.8 - - - +
45B LYS* 4.1 8.5 - - - -
72B THR* 4.1 13.5 - - + +
73B VAL* 1.3 80.3 - - - +
75B GLU* 1.3 64.2 + - - +
76B THR* 3.2 17.6 + - + +
294B TYR* 4.3 2.2 - - - -
295B THR* 2.9 40.2 + - - +
297B VAL* 4.4 5.2 - - + -
301B VAL* 4.2 30.5 - - + -
309B VAL* 3.7 27.6 - - + -
311B PHE* 3.9 17.3 - - + -
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Residues in contact with GLU 75 (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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43B GLY* 3.2 2.8 - - - -
44B TYR* 2.9 36.4 + - + +
46B ALA* 4.6 1.6 - - + -
73B VAL 4.3 0.8 + - - -
74B ILE* 1.3 68.9 - - - +
76B THR* 1.3 57.8 + - - +
77B PRO* 3.2 14.8 - - + +
151B VAL* 3.3 23.7 - - + +
152B PRO* 4.9 7.2 - - - +
153B SER* 4.3 3.3 + - - -
287B TYR* 2.5 36.6 + - + +
289B GLU 4.3 3.2 - - - +
290B VAL* 3.8 39.9 - - + +
291B ASP 4.4 4.5 + - - -
292B GLY* 4.9 4.5 + - - -
293B PRO* 3.5 12.8 - - - +
294B TYR* 4.2 1.1 - - - +
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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
------------------------------------------------------------
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