Contacts of the strand formed by residues 251 - 259 (chain A) in PDB entry 4II9
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 LYS 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLN* 3.5 21.8 + - - +
26A VAL 6.1 1.1 - - - +
110A GLU* 2.9 33.5 + - - +
149A VAL* 6.3 0.2 - - + -
246A LEU 3.8 0.7 - - - +
247A LYS* 3.6 1.9 - - - +
248A TYR* 3.0 38.8 + - + +
249A GLY 3.2 1.6 + - - +
250A ARG* 1.4 80.5 - - - +
252A ILE* 1.3 67.2 + - - +
253A TRP* 3.7 29.8 - - + -
284A THR* 3.5 6.8 - - - +
286A LEU* 3.2 29.4 - - + +
288A ASP* 2.9 34.7 + - + -
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Residues in contact with ILE 252 (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 ALA* 3.9 15.7 - - + -
246A LEU 3.4 4.0 - - - +
247A LYS* 3.7 20.2 - - + -
251A LYS* 1.3 75.4 - - - +
253A TRP* 1.4 61.0 + - - +
275A MET* 4.5 3.4 - - + +
278A TRP* 3.6 41.1 - - + -
279A ALA* 3.5 33.9 - - + +
282A THR* 4.0 8.1 - - - +
284A THR* 4.1 8.7 - - + -
286A LEU 3.0 6.3 + - - -
287A TYR* 3.3 25.7 - - + -
288A ASP* 2.9 24.3 + - - +
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Residues in contact with TRP 253 (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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25A GLN* 4.6 3.1 - - - -
26A VAL* 3.9 25.1 - - + -
27A THR* 3.9 10.3 - - + -
75A LYS* 3.5 36.8 - - + -
143A GLN* 5.3 1.1 - - - -
245A ALA* 3.1 5.6 - - - -
246A LEU 2.8 38.5 + - - +
251A LYS* 3.7 29.1 - - + -
252A ILE* 1.4 73.5 - - - +
254A TYR* 1.3 77.7 + - - +
255A MET* 3.3 33.1 + - + +
288A ASP* 3.5 27.2 + - - -
290A GLY* 4.3 10.4 - - - -
7B DAL 3.8 28.3 - - + -
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Residues in contact with TYR 254 (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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243A GLY* 4.7 3.6 - - - -
244A ILE 3.8 3.6 - - - -
245A ALA* 4.4 3.1 - - - +
252A ILE 4.1 0.8 + - - -
253A TRP* 1.3 79.3 + - - +
255A MET* 1.4 61.6 - - - +
256A TYR 3.6 11.4 - - - -
257A ALA* 3.3 35.4 - - + +
271A VAL* 5.7 0.4 - - + -
272A GLN* 3.6 29.8 - - - -
275A MET* 3.8 13.9 - - + -
287A TYR* 3.4 21.3 - - + +
288A ASP 2.8 14.6 + - - +
289A LEU* 3.7 32.3 - - + +
290A GLY* 4.9 0.3 - - - -
304A PHE* 4.5 14.7 - + - -
305A LYS* 4.5 12.8 - - - -
9C C 5.7 0.7 + - - -
10C A9Z 3.8 21.4 + - - -
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Residues in contact with MET 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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26A VAL* 4.2 6.1 - - - -
32A TRP* 3.9 25.1 - - + -
219A MET* 4.9 2.5 - - - -
244A ILE* 2.9 11.2 + - + +
246A LEU* 3.5 38.6 - - + -
253A TRP* 3.4 49.6 - - + +
254A TYR* 1.4 75.0 - - - +
256A TYR* 1.3 98.8 + - + +
5B CYS* 5.9 1.2 - - - +
7B DAL 4.3 16.1 - - + -
10C A9Z 4.9 14.3 + - - +
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Residues in contact with TYR 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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195A PHE* 3.8 17.7 - - + -
199A TYR* 4.0 21.3 - + - -
211A ARG* 2.9 22.7 + - - -
215A TYR* 3.6 0.3 - - - -
216A PHE* 3.8 35.9 - + - -
219A MET* 4.4 10.3 - - + -
243A GLY* 3.2 2.9 - - - -
244A ILE* 2.8 37.1 + - + -
254A TYR* 3.6 5.9 - - - -
255A MET* 1.3 112.0 - - + +
257A ALA* 1.3 62.5 + - - +
5B CYS* 6.6 0.2 - - + -
6B DAL 3.6 4.8 + - - -
7B DAL 2.4 30.4 + - - -
10C A9Z 4.1 6.1 - - - -
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Residues in contact with ALA 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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195A PHE* 4.1 7.4 - - - -
199A TYR* 3.7 6.8 - - - -
202A MET* 3.7 11.3 - - - +
242A THR 3.4 14.6 - - - +
243A GLY* 4.0 1.1 - - - -
254A TYR* 3.3 29.2 - - + +
256A TYR* 1.3 80.7 - - - +
258A GLY* 1.3 61.3 + - - +
10C A9Z 3.4 32.9 + - - +
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Residues in contact with GLY 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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195A PHE* 4.4 0.2 - - - -
198A THR* 3.4 29.6 + - - -
199A TYR* 3.9 2.5 - - - -
202A MET* 4.0 7.6 - - - -
241A SER* 3.3 2.1 - - - -
242A THR* 2.9 34.5 + - - +
257A ALA* 1.3 77.6 - - - +
259A SER* 1.3 63.9 + - - -
10C A9Z 4.1 4.1 + - - -
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Residues in contact with SER 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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198A THR* 3.3 16.4 + - - +
201A THR* 4.0 0.7 - - - +
202A MET* 3.7 5.4 + - - +
205A ARG* 2.8 41.4 + - - -
240A LEU 3.4 12.6 - - - -
241A SER* 3.7 10.3 - - - +
258A GLY* 1.3 76.5 - - - -
260A MET* 1.3 65.0 + - - +
264A THR* 4.2 11.0 - - - +
268A PRO* 4.6 4.7 - - - -
9C C 4.4 4.7 - - - +
10C A9Z 2.7 23.4 + - - -
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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