Contacts of the strand formed by residues 309 - 319 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ASN* 3.7 2.8 + - - -
105A PHE* 2.9 42.3 + - + +
179A SER* 3.3 3.1 - - - -
184A PHE* 3.2 10.7 - - - +
185A ALA 2.6 47.0 + - - +
235A PHE* 3.3 32.9 - - + +
301A VAL* 4.9 1.4 - - - +
302A SER 4.5 1.4 - - - +
303A ALA* 3.3 23.5 + - + +
307A ALA* 3.6 7.1 + - - +
308A VAL* 1.3 70.6 - - - +
310A SER* 1.3 64.3 + - - +
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Residues in contact with SER 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ILE 3.3 6.3 - - - -
104A ASN* 3.1 27.9 + - - -
105A PHE* 4.8 0.2 - - - -
177A PRO* 3.4 4.5 - - - +
178A THR* 2.7 39.3 + - - -
179A SER* 2.8 21.0 + - - -
183A GLN* 5.2 0.5 + - - -
235A PHE* 3.5 4.4 - - - -
308A VAL* 3.9 12.1 + - - +
309A ASN* 1.3 75.3 - - - +
311A ALA* 1.3 58.1 - - - +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 3.3 4.2 - - - -
103A ILE* 2.7 41.2 + - + +
105A PHE* 4.0 15.5 - - + -
175A ILE* 3.7 30.3 - - + -
176A TYR 3.5 7.6 - - - +
177A PRO* 3.9 9.0 - - + -
178A THR* 3.8 5.7 + - - -
235A PHE* 4.3 2.7 - - + -
310A SER* 1.3 76.1 - - - +
312A ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 3.9 24.7 - - + +
101A GLN 3.5 11.4 - - - +
102A SER* 4.7 10.8 - - - +
174A GLY 3.7 2.8 - - - +
175A ILE* 3.7 1.9 - - - -
176A TYR* 3.2 40.5 + - + +
178A THR* 3.8 24.9 - - + +
311A ALA* 1.3 76.6 - - - +
313A LEU* 1.3 66.1 + - - +
314A LYS* 3.7 7.0 + - + +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.3 7.4 - - - +
100A ASN 3.6 0.2 - - - -
101A GLN* 2.6 43.8 + - + +
103A ILE* 4.0 22.4 - - + -
113A ILE* 3.5 42.8 - - + -
123A TYR* 4.3 22.4 - - + -
173A VAL* 4.4 10.1 - - + -
174A GLY 3.5 6.7 - - - +
175A ILE* 4.3 13.7 - - + +
299A ILE* 6.2 0.2 - - + -
311A ALA 4.0 0.2 - - - -
312A ILE* 1.3 72.9 - - - +
314A LYS* 1.3 74.3 + - - +
315A THR* 4.2 10.8 - - + -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PRO* 5.6 1.1 - - - -
98A VAL* 3.9 18.7 - - + +
99A LEU 3.0 3.1 - - - +
100A ASN* 3.2 42.2 + - - +
173A VAL* 3.9 0.3 - - - +
174A GLY 2.9 28.7 + - - +
176A TYR* 3.9 17.9 - - + -
312A ILE* 3.7 6.0 + - + -
313A LEU* 1.3 79.1 - - - +
315A THR* 1.3 61.7 + - - +
316A TRP* 3.2 46.2 - - + +
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A VAL* 3.3 2.1 - - - -
99A LEU* 2.8 32.9 + - + -
115A ILE* 4.1 13.7 - - - +
122A ALA* 3.2 46.5 + - + +
123A TYR* 4.7 3.4 - - + -
145A PHE* 2.7 35.2 - - + -
172A ASN 3.5 12.9 + - - -
173A VAL* 4.7 2.2 - - - -
313A LEU* 4.2 8.7 - - + -
314A LYS* 1.3 78.7 - - - +
316A TRP* 1.3 61.7 + - - +
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Residues in contact with TRP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A CYS* 6.3 1.8 - - - -
73A PRO* 3.7 29.7 + - + +
74A PRO* 3.4 29.0 - - + +
79A ASP* 5.2 6.7 - - - -
97A ASP 3.2 6.3 - - - +
98A VAL* 3.8 24.8 - - + +
145A PHE* 4.1 0.6 - - - -
170A SER* 5.2 2.7 - - - +
171A MET* 3.3 4.2 - - - +
172A ASN* 2.9 55.9 + - + +
173A VAL 4.1 0.2 - - - -
174A GLY 4.0 17.9 - - - -
176A TYR* 3.4 23.3 - - - -
240A PHE* 3.7 15.5 - + - -
314A LYS* 3.2 40.9 - - + +
315A THR* 1.3 79.9 + - - +
317A ALA* 1.3 64.1 + - - +
318A CYS 5.6 0.2 - - - +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LYS* 4.8 0.2 - - - -
97A ASP* 2.9 32.7 + - + +
145A PHE* 3.9 22.7 - - + -
168A TYR* 4.3 10.5 - - + -
170A SER* 3.2 15.0 - - - +
171A MET* 4.6 5.4 - - + -
316A TRP* 1.3 77.8 - - - +
318A CYS* 1.3 60.9 - - - +
319A LEU* 3.5 17.3 - - + +
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Residues in contact with CYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A CYS* 3.4 20.2 - - - -
79A ASP* 5.0 0.2 - - - +
81A GLY* 5.3 4.5 - - - -
83A GLY 5.3 1.8 - - - -
94A THR* 3.4 20.6 - - - -
95A ARG 3.3 4.0 - - - -
96A LYS* 3.4 31.0 - - + +
168A TYR 3.9 0.2 - - - -
169A ALA* 2.8 42.5 + - + -
170A SER* 3.0 29.5 + - - +
317A ALA* 1.3 74.6 - - - +
319A LEU* 1.3 60.0 - - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 2.6 31.0 - - - +
95A ARG* 2.8 26.4 + - + +
97A ASP* 3.5 18.2 - - - +
119A PRO* 4.3 5.8 - - + -
166A PHE* 4.0 25.6 - - + -
167A ARG 3.6 7.4 - - - +
168A TYR* 4.0 24.5 - - + +
169A ALA* 4.3 2.0 - - - +
317A ALA* 3.5 28.9 - - + +
318A CYS* 1.3 79.3 - - - +
320A GLU* 1.3 59.6 + - - +
321A TYR* 3.6 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