Contacts of the strand formed by residues 63 - 75 (chain B) in PDB entry 2VDE
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 GLN 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A TYR 3.7 2.0 - - - -
316A GLN* 2.8 47.1 + - + +
317A GLY 3.6 0.6 - - - +
319A MET* 5.9 2.6 - - - +
58B SER* 2.8 32.3 + - - -
59B PRO* 3.9 9.9 - - + +
61B LEU 3.4 11.4 + - - +
62B PRO* 1.3 72.6 + - - +
64B LEU* 1.3 59.3 + - - +
65B GLY 3.8 1.4 + - - -
92B GLN 3.6 1.6 - - - +
93B LEU* 3.2 6.0 - - - +
94B THR* 2.8 52.2 + - - +
95B GLN* 5.9 0.2 - - - -
102B LYS* 6.2 1.1 - - - +
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Residues in contact with LEU 64 (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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313A PRO* 4.2 0.7 - - - +
314A ILE* 2.9 53.7 + - + +
315A TYR* 2.6 33.4 + - + +
316A GLN* 5.0 0.2 - - - +
62B PRO* 4.1 1.5 - - + -
63B GLN* 1.3 72.0 - - - +
65B GLY* 1.3 62.0 + - - +
91B LEU* 5.2 12.1 - - + -
92B GLN 3.3 14.6 - - - +
93B LEU* 4.0 26.0 - - + -
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Residues in contact with GLY 65 (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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312A LEU 3.9 5.8 - - - -
313A PRO* 4.4 6.3 - - - -
314A ILE* 4.2 4.5 - - - +
63B GLN 3.8 2.2 + - - -
64B LEU* 1.3 76.8 - - - +
66B LEU* 1.3 58.7 + - - +
91B LEU* 3.8 2.6 - - - +
92B GLN* 2.7 45.1 + - - +
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Residues in contact with LEU 66 (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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310A PHE* 5.7 5.4 - - + -
311A SER* 3.7 2.4 - - - -
312A LEU* 2.8 47.8 + - + +
314A ILE* 3.4 27.8 - - + -
65B GLY* 1.3 73.2 - - - +
67B GLY* 1.3 67.7 + - - +
68B ALA 5.1 0.4 - - - +
89B ALA* 5.2 4.7 - - + -
90B SER 3.2 37.9 - - - +
91B LEU* 4.1 12.3 - - + +
92B GLN* 4.6 2.0 - - - +
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE* 3.3 17.5 - - - -
311A SER* 4.3 0.7 - - - -
66B LEU* 1.3 82.6 - - - +
68B ALA* 1.3 61.6 + - - -
69B ASP* 5.3 0.7 - - - +
88B SER 4.0 0.9 - - - +
89B ALA* 3.6 2.0 - - - -
90B SER* 3.2 36.1 + - - -
92B GLN* 5.7 0.8 - - - +
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Residues in contact with ALA 68 (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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309A SER* 3.9 0.7 + - - -
310A PHE* 3.0 48.8 + - + +
66B LEU* 5.1 0.8 - - - +
67B GLY* 1.3 73.4 - - - -
69B ASP* 1.3 66.5 + - - +
88B SER 3.1 10.3 - - - +
89B ALA* 4.1 9.9 - - + +
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Residues in contact with ASP 69 (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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308A LEU 3.1 20.6 - - - +
309A SER* 3.8 15.1 + - - +
67B GLY 5.3 0.9 - - - +
68B ALA* 1.3 80.0 - - - +
70B TYR* 1.3 65.1 + - - +
71B THR* 4.7 7.2 - - - +
86B ALA 3.6 5.0 - - - +
87B THR* 3.8 0.6 - - - -
88B SER* 2.7 42.5 + - - +
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Residues in contact with TYR 70 (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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306A VAL* 4.6 4.7 - - + -
307A GLY* 3.4 2.5 - - - -
308A LEU* 2.9 57.0 + - + +
69B ASP* 1.3 76.9 - - - +
71B THR* 1.3 86.1 + - - +
72B TYR* 3.9 21.7 - - + +
85B ASN* 3.9 20.8 + - + +
86B ALA 3.5 3.8 - - - -
87B THR* 3.6 28.5 - - + +
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Residues in contact with THR 71 (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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305A LYS* 4.6 12.3 - - - +
306A VAL 3.5 13.4 + - - -
307A GLY* 3.9 3.1 - - - -
69B ASP* 4.7 8.3 - - - +
70B TYR* 1.3 83.8 - - - +
72B TYR* 1.3 66.3 + - - +
73B SER* 5.2 2.2 + - - +
85B ASN* 3.3 6.9 - - - +
86B ALA* 3.0 48.0 + - + +
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Residues in contact with TYR 72 (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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304A ASN 3.3 4.4 - - - +
305A LYS* 3.0 26.5 - - - +
306A VAL* 2.9 34.8 + - + +
70B TYR* 3.9 16.4 - - + +
71B THR* 1.3 81.1 + - - +
73B SER* 1.3 78.4 + - - +
74B ASN* 3.6 21.5 + - + -
83B ASN* 3.9 16.8 + - + -
84B SER 3.5 13.9 - - - -
85B ASN* 3.8 20.6 - - - +
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Residues in contact with SER 73 (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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303A GLN* 3.5 27.8 + - - -
304A ASN 3.3 6.5 - - - -
305A LYS* 4.0 12.5 - - - +
71B THR* 4.4 1.9 + - - +
72B TYR* 1.3 89.0 - - - +
74B ASN* 1.3 61.8 + - - +
83B ASN* 3.2 17.8 - - - +
84B SER* 2.9 33.7 + - - +
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Residues in contact with ASN 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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303A GLN* 3.3 24.8 - - - +
304A ASN* 3.0 34.4 + - + +
72B TYR* 3.6 23.6 + - + -
73B SER* 1.3 76.3 - - - +
75B GLY* 1.3 81.7 + - - +
76B TYR* 3.1 9.2 + - - +
82B ILE 3.9 4.9 - - - -
83B ASN* 3.8 11.5 + - - +
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Residues in contact with GLY 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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74B ASN* 1.3 80.7 + - - +
76B TYR* 1.3 63.0 + - - -
77B ARG 3.4 2.2 + - - -
79B ALA* 3.4 33.4 - - - -
80B ASN* 3.5 25.1 - - - +
81B GLY 4.7 1.3 + - - +
82B ILE 3.4 7.7 + - - -
83B ASN* 4.2 3.2 - - - +
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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