Contacts of the strand formed by residues 309 - 319 (chain B) in PDB entry 2BBV
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 ASN 309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ASN* 3.5 3.8 - - - +
105B PHE* 2.9 38.1 + - + +
179B SER* 3.4 3.6 - - - -
184B PHE* 3.2 8.8 - - - +
185B ALA 2.6 51.0 + - - -
235B PHE* 3.6 31.2 - - + -
301B VAL* 4.7 2.4 - - - +
302B SER 3.7 6.7 + - - -
303B ALA* 3.1 22.8 - - + +
307B ALA* 3.7 3.5 + - - +
308B VAL* 1.3 70.5 - - - +
310B SER* 1.3 61.9 + - - +
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Residues in contact with SER 310 (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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103B ILE 3.3 7.9 - - - -
104B ASN* 2.8 29.0 + - - -
105B PHE* 4.9 0.2 - - - -
177B PRO* 3.5 3.3 - - - +
178B THR* 2.8 42.9 + - - +
179B SER* 2.9 15.4 + - - -
183B GLN* 4.7 1.2 + - - -
235B PHE* 3.5 3.8 - - - -
308B VAL* 4.2 11.1 - - - +
309B ASN* 1.3 73.9 - - - +
311B ALA* 1.3 60.9 - - - +
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Residues in contact with ALA 311 (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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101B GLN 3.4 0.2 - - - +
102B SER* 3.5 3.3 - - - -
103B ILE* 2.9 40.4 + - + +
105B PHE* 3.9 13.9 - - + -
175B ILE* 3.4 31.2 - - + -
176B TYR 3.3 14.6 - - - +
177B PRO* 4.0 2.7 - - + -
178B THR* 4.1 5.4 - - - +
235B PHE* 4.0 2.9 - - + -
310B SER* 1.3 78.2 - - - +
312B ILE* 1.3 65.3 + - - +
313B LEU 3.8 0.2 - - - -
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Residues in contact with ILE 312 (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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100B ASN* 4.1 22.2 - - + +
101B GLN 3.3 6.3 - - - +
102B SER* 3.5 27.8 - - - +
174B GLY 3.5 1.6 - - - +
175B ILE* 3.5 5.5 - - - -
176B TYR* 2.9 50.4 + - + +
178B THR* 4.5 9.2 - - - +
311B ALA* 1.3 74.3 - - - +
313B LEU* 1.3 72.2 + - - +
314B LYS* 4.5 6.3 - - + -
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Residues in contact with LEU 313 (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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99B LEU* 3.6 3.6 - - + +
100B ASN* 3.4 2.6 - - - -
101B GLN* 2.6 48.9 + - + +
103B ILE* 3.8 23.3 - - + -
105B PHE* 5.1 1.3 - - + -
113B ILE* 3.8 34.5 - - + -
115B ILE* 5.3 0.2 - - + -
123B TYR* 4.2 31.4 - - + -
173B VAL* 4.7 7.2 - - + -
174B GLY 3.8 5.6 - - - +
175B ILE* 4.7 14.8 - - + +
299B ILE* 6.3 0.2 - - + -
311B ALA 3.8 1.6 + - - -
312B ILE* 1.3 74.7 - - - +
314B LYS* 1.3 64.3 + - - +
315B THR* 3.3 24.2 - - - +
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Residues in contact with LYS 314 (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 PRO* 6.0 1.4 - - - +
98B VAL* 4.0 9.6 - - - +
99B LEU 3.0 5.6 - - - +
100B ASN* 3.5 43.4 + - - +
173B VAL* 3.4 4.9 - - - +
174B GLY 2.9 38.2 + - - +
176B TYR* 4.0 15.7 - - + -
312B ILE* 4.5 4.7 - - + -
313B LEU* 1.3 74.0 - - - +
315B THR* 1.3 61.7 + - - +
316B TRP* 3.1 50.7 - - + +
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Residues in contact with THR 315 (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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98B VAL* 3.2 9.5 - - - +
99B LEU* 2.9 31.9 + - - +
115B ILE* 3.9 23.5 - - + +
122B ALA* 3.9 23.1 - - - +
123B TYR* 4.4 5.7 - - - -
145B PHE* 3.3 18.0 - - + -
171B MET* 5.6 0.7 - - + -
172B ASN 3.0 21.8 - - - +
313B LEU* 3.3 21.7 - - - +
314B LYS* 1.3 70.9 + - - +
316B TRP* 1.3 68.2 + - - +
317B ALA* 5.6 0.2 - - + -
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Residues in contact with TRP 316 (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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73B PRO* 3.7 28.1 - - + +
74B PRO* 3.6 27.6 - - + +
79B ASP* 4.8 7.9 - - - +
97B ASP 3.4 6.1 - - - +
98B VAL* 3.9 21.8 - - + +
145B PHE* 4.2 2.2 - - - -
170B SER* 4.9 2.2 - - - +
171B MET* 3.2 3.7 - - - +
172B ASN* 2.7 64.5 + - + +
173B VAL 3.7 0.4 - - - -
174B GLY 3.8 16.6 - - - -
176B TYR* 3.6 22.2 - - - -
240B PHE* 3.5 17.7 - + - -
314B LYS* 3.1 46.7 - - + +
315B THR* 1.3 79.4 - - - +
317B ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 317 (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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95B ARG 3.5 3.5 - - - +
96B LYS* 4.7 0.9 - - - -
97B ASP* 3.1 31.1 + - + +
145B PHE* 3.9 21.5 - - + -
168B TYR* 4.0 11.0 - - + +
170B SER* 3.1 14.1 - - - +
171B MET* 4.5 5.6 - - + -
315B THR* 5.6 0.9 - - + -
316B TRP* 1.3 77.7 - - - +
318B CYS* 1.3 61.2 + - - +
319B LEU* 3.5 16.9 - - + +
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Residues in contact with CYS 318 (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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69B CYS* 3.3 30.3 - - - -
81B GLY* 5.0 6.3 - - - -
83B GLY* 5.5 2.9 - - - -
94B THR* 4.7 10.3 - - - -
95B ARG 3.4 6.5 - - - -
96B LYS* 3.8 28.0 - - + +
168B TYR* 3.9 0.3 - - - -
169B ALA* 2.9 33.7 + - + -
170B SER* 2.9 24.4 + - - +
317B ALA* 1.3 72.3 - - - +
319B LEU* 1.3 74.2 + - - +
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Residues in contact with LEU 319 (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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93B VAL 3.5 0.9 - - - +
94B THR* 3.0 6.6 - - - -
95B ARG* 2.6 42.0 + - - +
97B ASP* 4.0 9.6 - - - +
119B PRO* 4.1 16.6 - - + -
166B PHE* 4.1 16.2 - - + -
167B ARG 3.2 16.4 - - - +
168B TYR* 3.7 23.3 - - + +
169B ALA* 4.4 1.8 - - - +
317B ALA* 3.5 23.1 - - + +
318B CYS* 1.3 83.8 - - - +
320B GLU* 1.3 63.8 + - - +
321B TYR* 3.3 38.1 - - + +
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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
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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