Contacts of the strand formed by residues 265 - 271 (chain B) in PDB entry 4NAW
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 LEU 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B ILE* 4.2 9.2 - - + -
186B PRO 2.9 15.4 + - - +
187B PHE* 3.2 8.4 - - + +
188B ARG 2.9 27.5 + - - +
240B ILE* 4.3 22.0 - - + -
251B LEU* 3.9 26.0 - - + -
254B LEU* 3.8 15.3 - - + +
255B SER* 3.8 23.3 - - - +
258B LEU* 3.6 31.0 - - + +
259B SER* 3.8 10.5 + - - +
264B PHE* 1.3 70.0 - - - +
266B HIS* 1.3 63.6 + - - +
267B ILE* 3.6 11.4 + - + +
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Residues in contact with HIS 266 (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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82B PRO* 4.0 16.4 - - + +
85B LEU* 3.9 25.2 - - + +
128B CYS* 6.4 0.2 - - - -
188B ARG* 3.6 18.8 - - - +
190B TYR* 3.0 28.1 + - + -
239B MET 4.4 2.1 - - - +
240B ILE* 3.9 18.8 - - - +
241B HIS 5.0 0.2 + - - -
260B TYR* 3.4 48.2 + + + -
262B ASP* 2.8 25.2 + - - -
264B PHE* 3.4 27.0 + + + +
265B LEU* 1.3 71.4 - - - +
267B ILE* 1.3 60.0 + - - +
268B SER 4.3 0.7 + - - -
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 4.7 3.1 - - + -
188B ARG 2.8 12.2 + - - +
189B ILE* 3.3 19.1 - - + +
190B TYR* 2.7 35.6 + - - -
215B LEU* 4.2 14.1 - - + -
218B LEU* 4.2 24.9 - - + -
219B LEU* 5.2 2.7 - - + -
238B VAL* 3.5 30.3 - - + -
239B MET 3.9 2.2 - - - -
240B ILE* 3.9 17.9 - - + -
265B LEU* 3.8 24.0 - - + +
266B HIS* 1.3 77.7 - - - +
268B SER* 1.3 61.9 + - - +
269B ILE* 4.3 9.4 - - + -
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Residues in contact with SER 268 (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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85B LEU* 3.4 24.6 - - - +
88B ASP* 4.0 9.1 - - - +
89B LEU* 3.8 20.2 + - - +
190B TYR 3.7 4.5 - - - +
237B GLN 3.6 0.9 - - - +
238B VAL* 3.5 4.0 - - - -
239B MET* 2.8 49.9 + - - +
266B HIS 4.3 0.4 + - - -
267B ILE* 1.3 72.4 - - - +
269B ILE* 1.3 62.6 + - - +
270B ILE* 4.0 17.5 - - - -
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Residues in contact with ILE 269 (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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89B LEU* 4.7 2.1 - - - +
189B ILE* 3.7 29.6 - - + -
190B TYR 2.9 12.2 + - - +
191B GLN* 3.8 37.6 - - + +
192B THR* 4.7 2.4 + - - +
219B LEU* 4.5 7.0 - - + -
223B CYS* 4.6 4.0 - - - -
226B ALA* 4.2 17.5 - - + -
236B ASN* 3.8 32.1 - - + +
237B GLN 3.6 3.6 - - - +
238B VAL* 4.0 28.7 - - + -
267B ILE* 4.3 3.8 - - + -
268B SER* 1.3 78.1 - - - +
270B ILE* 1.3 66.5 + - - +
271B PRO* 4.7 1.0 - - - +
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Residues in contact with ILE 270 (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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88B ASP 4.0 14.8 - - - +
89B LEU* 4.3 15.5 - - + +
92B SER* 3.8 14.1 - - - +
93B SER* 6.2 2.9 - - - -
192B THR* 6.3 0.4 - - + -
236B ASN* 3.5 5.9 - - - -
237B GLN* 2.8 65.4 + - + +
239B MET* 3.6 28.9 - - + -
268B SER* 4.1 15.9 - - - -
269B ILE* 1.3 80.8 - - - +
271B PRO* 1.3 73.8 - - + +
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Residues in contact with PRO 271 (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 SER* 6.1 0.9 - - - -
192B THR* 5.4 7.2 - - - +
193B THR* 6.0 7.0 - - + -
235B LYS 3.7 1.6 - - - +
236B ASN* 3.5 13.7 - - - +
237B GLN* 3.9 0.3 - - - +
269B ILE 4.7 1.1 - - - +
270B ILE* 1.3 98.9 - - + +
272B GLN* 1.3 67.1 + - - +
273B PRO* 3.4 7.3 - - - +
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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