Contacts of the strand formed by residues 254 - 265 (chain A) in PDB entry 4B7B
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 GLU 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A LYS* 3.0 45.0 + - + +
247A GLU 3.3 3.8 - - - +
248A THR* 4.4 10.5 + - + +
252A GLY 4.0 8.0 - - - +
253A GLU* 1.3 83.8 - - - +
255A LEU* 1.3 68.0 + - - +
256A VAL* 4.1 5.7 + - + +
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Residues in contact with LEU 255 (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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245A MET 3.7 0.9 - - - +
246A LYS* 3.2 4.2 - - - -
247A GLU* 2.7 65.9 + - + +
249A THR* 4.0 16.6 - - + -
253A GLU* 3.5 31.6 - - + +
254A GLU* 1.3 83.5 - - - +
256A VAL* 1.3 62.2 + - - +
257A LYS* 4.1 25.1 + - + +
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Residues in contact with VAL 256 (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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244A HIS* 6.4 0.7 - - + -
245A MET 3.4 8.3 - - - +
246A LYS* 4.1 26.5 - - + -
254A GLU* 4.2 6.3 + - + +
255A LEU* 1.3 79.9 - - - +
257A LYS* 1.3 73.9 + - - +
258A ILE* 5.3 8.7 - - + -
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Residues in contact with LYS 257 (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 ILE 4.3 5.8 - - - +
95A MET* 4.0 30.3 - - - +
96A GLY* 4.3 5.8 - - - -
245A MET* 2.8 54.1 + - + +
247A GLU* 6.4 2.0 - - + -
255A LEU* 4.1 29.5 + - + +
256A VAL* 1.3 78.7 + - - +
258A ILE* 1.3 68.2 + - - +
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Residues in contact with ILE 258 (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 GLY* 3.1 23.0 + - - +
97A TYR 4.4 0.7 - - - +
98A ASN* 5.0 4.6 + - - +
242A THR* 3.9 25.6 - - + -
243A ILE 3.4 4.7 - - - +
244A HIS* 3.5 32.8 - - + +
256A VAL* 5.3 8.3 - - + -
257A LYS* 1.3 80.6 - - - +
259A GLY* 1.3 61.7 + - - +
260A LYS* 5.9 0.9 - - + -
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Residues in contact with GLY 259 (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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93A VAL* 3.1 31.9 - - - -
97A TYR 3.5 3.8 - - - -
242A THR* 3.5 5.7 - - - +
243A ILE* 3.0 34.1 + - - -
245A MET* 3.4 6.3 - - - +
258A ILE* 1.3 76.4 - - - +
260A LYS* 1.3 62.9 - - - +
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Residues in contact with LYS 260 (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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93A VAL* 3.5 10.3 - - - +
97A TYR 3.0 8.1 + - - -
98A ASN* 3.0 33.5 - - - +
99A CYS 2.7 31.9 + - - -
159A SER* 5.7 0.6 + - - -
201A GLU* 5.7 3.0 + - - -
240A SER* 4.0 16.2 + - - -
241A VAL 3.2 14.8 - - - +
242A THR* 3.8 19.3 + - + +
258A ILE* 5.9 0.4 - - + -
259A GLY* 1.3 74.8 - - - +
261A LEU* 1.3 58.2 + - - +
262A ASN* 3.5 25.1 - - - +
323A SER* 5.4 0.4 - - - -
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Residues in contact with LEU 261 (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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86A VAL* 4.9 9.0 - - + -
89A ILE* 4.5 6.3 - - + -
90A LEU* 4.5 11.0 - - + -
93A VAL* 3.8 21.0 - - + +
99A CYS 3.5 13.7 - - - +
101A ILE* 4.1 11.7 - - + -
139A THR* 3.7 32.1 - - + +
143A ILE* 6.2 0.7 - - + -
239A PHE 3.7 1.9 - - - +
240A SER* 3.4 3.1 - - - -
241A VAL* 2.9 48.1 + - + +
260A LYS* 1.3 74.8 - - - +
262A ASN* 1.3 76.2 + - - +
263A LEU* 3.6 32.9 - - + +
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Residues in contact with ASN 262 (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 ASN* 4.7 0.8 + - - -
99A CYS 2.9 22.6 + - - +
100A THR* 3.3 16.3 + - + +
101A ILE 2.9 29.3 + - - +
238A VAL* 4.7 1.3 - - + -
239A PHE 3.6 3.1 - - - +
240A SER* 2.6 26.8 + - - +
260A LYS* 3.5 19.6 - - - +
261A LEU* 1.3 73.5 - - - +
263A LEU* 1.3 64.0 + - - +
264A VAL* 3.9 6.1 - - + -
320A LEU* 4.2 18.5 - - + +
323A SER* 2.6 30.3 + - - -
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Residues in contact with LEU 263 (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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101A ILE* 3.6 21.1 - - + -
115A MET* 3.8 16.3 - - - +
135A ILE* 3.9 24.2 - - + -
136A ILE* 3.7 31.4 - - + +
139A THR* 4.2 9.6 - - + +
237A SER 3.9 1.7 - - - +
239A PHE* 2.7 45.3 + - + +
241A VAL* 4.8 5.8 - - + -
261A LEU* 3.6 38.8 - - + +
262A ASN* 1.3 73.5 - - - +
264A VAL* 1.3 61.7 + - - +
265A ASP* 4.1 0.9 + - - +
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Residues in contact with VAL 264 (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 THR* 4.3 12.1 - - + -
101A ILE 3.0 6.6 + - - +
102A PHE* 3.7 26.4 - - + -
103A ALA 2.9 27.0 + - - -
115A MET* 3.9 6.1 - - - +
236A HIS* 4.9 1.6 - - + -
237A SER 3.3 10.1 - - - +
238A VAL* 4.0 24.0 - - + -
262A ASN* 4.4 2.0 - - + -
263A LEU* 1.3 77.4 - - - +
265A ASP* 1.3 63.4 + - - +
266A LEU* 3.4 32.2 + - + -
316A LEU* 4.2 11.2 - - + -
320A LEU* 4.2 9.4 - - + -
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Residues in contact with ASP 265 (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 ALA* 4.2 2.0 - - - -
111A LYS* 3.1 30.3 - - - +
112A THR* 2.3 39.9 + - - +
115A MET* 4.3 14.8 - - + +
116A GLU* 5.0 4.0 - - - +
221A ARG* 5.9 0.5 + - - -
232A SER 6.2 0.2 - - - -
235A SER 3.8 2.1 - - - +
236A HIS* 3.7 0.7 - - - -
237A SER* 3.0 43.3 + - - +
263A LEU 4.1 2.2 + - - +
264A VAL* 1.3 71.6 - - - +
266A LEU* 1.3 65.8 + - - +
1364A ADP 4.6 0.2 + - - -
1372A CD 4.6 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
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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