Contacts of the strand formed by residues 89 - 96 (chain A) in PDB entry 4BC4
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 VAL 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A CYS* 3.4 16.2 - - - +
11A LEU* 3.9 24.5 - - + +
84A PHE* 3.8 27.6 - - + -
85A ASP 4.4 0.2 - - - +
86A PHE* 3.2 20.4 + - - +
87A SER 3.4 0.8 - - - -
88A GLN* 1.3 74.1 - - - +
90A LEU* 1.3 59.2 + - - +
91A ALA 3.5 21.5 - - - +
92A LEU* 4.8 0.9 - - + -
268A PHE* 4.1 14.4 - - + -
269A PRO* 3.2 23.4 - - - +
272A CYS* 3.6 17.8 - - - -
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Residues in contact with LEU 90 (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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8A ARG* 3.8 39.5 - - + +
9A CYS 2.8 14.6 + - - +
27A ALA* 6.0 1.6 - - + -
88A GLN* 4.3 4.3 - - - +
89A VAL* 1.3 73.5 - - - +
91A ALA* 1.3 61.2 + - - +
269A PRO* 5.3 4.0 - - + -
271A GLY 4.2 2.9 - - - +
272A CYS* 3.5 6.5 - - - +
273A LYS* 3.2 16.8 + - - +
478A PHE* 5.1 7.6 - - + -
481A LEU* 3.5 34.6 - - + +
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Residues in contact with ALA 91 (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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10A CYS* 3.2 31.9 - - - -
11A LEU 3.2 3.3 + - - -
89A VAL* 3.5 7.3 - - - +
90A LEU* 1.3 81.7 - - - +
92A LEU* 1.3 63.6 + - - +
272A CYS* 3.9 2.9 - - - -
273A LYS* 3.2 20.0 - - + +
275A VAL* 5.0 3.6 - - + -
477A ALA* 4.2 10.5 - - + +
481A LEU* 3.7 27.8 - - + -
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Residues in contact with LEU 92 (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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11A LEU* 3.3 22.9 - - + +
13A TRP* 4.1 11.0 - - + +
89A VAL* 4.8 0.4 - - + -
91A ALA* 1.3 77.2 - - - +
93A SER* 1.3 63.9 + - - +
204A PHE* 4.0 23.8 - - + -
258A ILE* 3.9 28.9 - - + -
268A PHE* 4.0 16.8 - - + -
272A CYS* 4.4 5.4 - - - -
273A LYS 2.9 11.4 + - - +
274A VAL* 4.3 10.5 - - + -
275A VAL* 3.0 26.0 + - - +
277A PHE* 3.8 26.5 - - + -
477A ALA* 3.8 4.7 - - - -
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Residues in contact with SER 93 (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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11A LEU 3.1 7.9 + - - +
12A GLY* 3.5 0.2 - - - -
13A TRP* 3.0 27.9 + - - -
92A LEU* 1.3 75.2 - - - +
94A GLY* 1.3 63.8 + - - +
275A VAL* 2.9 27.7 + - - -
276A ALA 3.0 2.9 + - - -
277A PHE* 3.6 14.1 - - - -
473A SER* 3.6 22.9 - - - -
476A ARG* 2.9 23.4 + - - -
477A ALA* 3.9 4.1 - - - +
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Residues in contact with GLY 94 (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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13A TRP 3.2 13.0 - - - -
93A SER* 1.3 83.0 + - - +
95A ALA* 1.3 59.0 + - - +
277A PHE* 3.3 28.2 - - - -
278A THR* 3.1 23.7 + - - +
473A SER* 3.1 13.2 + - - -
476A ARG* 4.0 2.6 + - - -
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Residues in contact with ALA 95 (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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13A TRP 2.8 9.4 + - - +
14A ASP* 3.4 9.9 - - - +
15A PHE* 2.8 36.1 + - - +
94A GLY* 1.3 75.5 - - - -
96A GLY* 1.3 55.5 + - - +
197A SER* 4.7 4.0 - - - -
277A PHE* 4.7 1.6 - - - -
278A THR 3.2 7.6 - - - +
280A ASP* 3.9 13.5 - - - -
283A ALA* 3.7 27.4 - - + -
469A ALA* 4.1 5.6 - - + -
473A SER* 3.7 4.0 - - - +
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Residues in contact with GLY 96 (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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15A PHE* 3.5 7.0 - - - -
95A ALA* 1.3 74.1 - - - +
97A GLN* 1.3 70.0 + - - +
98A GLN* 3.2 1.0 + - - -
196A VAL* 4.0 5.2 - - - -
197A SER* 3.9 23.3 - - - -
215A ASP* 4.3 0.7 - - - +
278A THR 3.0 8.7 + - - -
279A GLY* 3.4 6.4 - - - -
280A ASP* 2.9 23.2 + - - -
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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