Contacts of the strand formed by residues 330 - 340 (chain A) in PDB entry 4RZR
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 ILE 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A MET* 3.0 20.7 - - + +
254A ASN* 3.3 4.0 - - - -
255A SER 2.8 37.8 + - - +
261A ILE* 4.3 6.1 - - + -
288A ALA* 3.8 24.7 - - + -
289A VAL 3.7 5.8 - - - +
290A THR* 4.3 5.8 - - + +
319A LEU* 3.9 25.6 - - + -
322A ILE* 4.2 9.6 - - + -
323A LEU* 3.9 19.7 - - + -
328A ARG 4.4 6.7 - - - +
329A LYS* 1.3 75.9 - - - +
331A ARG* 1.3 64.0 + - - +
332A ARG 3.3 22.9 - - - +
333A ILE* 4.5 5.6 - - + -
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Residues in contact with ARG 331 (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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36A ARG* 3.6 32.5 - - - +
250A THR* 5.0 3.0 - - + +
251A MET* 2.9 33.5 + - - +
254A ASN* 3.3 27.3 - - - +
289A VAL* 2.7 15.4 + - + +
290A THR 3.7 12.6 - - - +
291A GLU* 4.1 10.0 + - - -
293A LEU* 3.7 29.1 - - + +
329A LYS 4.0 0.8 + - - -
330A ILE* 1.3 74.6 - - - +
332A ARG* 1.3 68.5 + - + +
5B 2JV 3.8 21.0 + - - +
6B G 2.7 37.0 + - - -
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Residues in contact with ARG 332 (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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248A ILE* 4.0 11.9 - - + -
249A VAL 3.2 11.0 - - - +
250A THR* 3.2 27.7 + - - +
251A MET* 4.5 0.4 - - - +
287A VAL 4.5 0.2 - - - -
288A ALA* 3.4 0.7 - - - -
289A VAL* 2.8 66.2 + - + +
293A LEU* 4.4 10.3 - - - +
330A ILE* 3.3 10.3 - - - +
331A ARG* 1.3 86.5 - - + +
333A ILE* 1.3 61.8 + - - +
5B 2JV 4.3 4.4 - - - +
6B G 3.0 48.5 + - - +
7B A 4.2 19.5 + - - -
101B TRS 3.2 27.7 + - - -
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Residues in contact with ILE 333 (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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248A ILE* 3.8 4.3 - - - -
249A VAL* 2.9 30.1 + - - +
251A MET* 4.0 8.1 - - + -
261A ILE* 3.8 27.6 - - + -
264A TYR* 3.5 31.2 - - + -
265A LEU* 4.0 20.0 - - + +
268A ALA* 4.8 0.6 - - - +
286A VAL* 3.8 20.6 - - + -
287A VAL 3.3 20.0 - - - +
288A ALA* 4.0 11.4 - - + -
319A LEU* 4.0 18.2 - - + -
330A ILE* 4.5 4.7 - - + -
332A ARG* 1.3 74.3 - - - +
334A GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 334 (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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247A ARG 3.1 13.7 - - - -
248A ILE* 3.8 6.7 - - - +
265A LEU* 3.8 4.0 - - - +
268A ALA* 4.3 8.7 - - - -
286A VAL* 3.4 7.1 - - - +
287A VAL* 3.0 31.6 + - - +
333A ILE* 1.3 79.2 - - - +
335A VAL* 1.3 70.9 + - - +
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Residues in contact with VAL 335 (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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246A GLY* 3.2 2.5 - - - -
247A ARG 2.8 36.4 + - - +
248A ILE* 5.0 0.4 - - - +
265A LEU* 3.6 18.2 - - + -
268A ALA* 4.1 2.7 - - + -
269A ILE* 3.8 26.9 - - + +
272A SER* 3.8 11.4 - - - +
284A ILE* 4.3 11.0 - - + -
285A HIS 3.1 13.0 - - - +
286A VAL* 4.0 11.4 - - + +
287A VAL* 4.6 1.5 - - - +
334A GLY* 1.3 80.1 - - - +
336A ARG* 1.3 68.2 + - - +
337A PHE* 3.7 25.1 - - + -
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Residues in contact with ARG 336 (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 SER* 2.9 30.9 + - - -
245A ILE 3.8 5.2 - - - +
246A GLY* 4.2 3.8 - - - -
284A ILE* 3.6 1.9 - - - -
285A HIS* 2.7 49.0 + - + +
287A VAL* 4.0 20.6 - - + -
335A VAL* 1.3 80.4 - - - +
337A PHE* 1.3 64.4 + - - +
338A SER* 6.4 0.2 - - - -
9B T 3.6 43.2 + - + +
10B G 2.7 50.5 + - - -
11B G 4.6 1.7 + - - -
8C C 3.8 13.3 - - - +
9C C 4.5 1.4 - - - +
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Residues in contact with PHE 337 (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 SER* 3.1 8.7 - - - -
245A ILE 2.8 41.8 + - - +
269A ILE* 4.3 7.4 - - + -
272A SER* 3.6 27.8 - - - -
273A TYR* 3.6 26.9 - + - -
276A LEU* 4.4 11.7 - - + -
281A PRO* 3.8 26.2 - - + -
283A ALA 3.4 13.7 - - - -
284A ILE* 3.6 37.0 - - + -
306A ILE* 5.2 2.7 - - + -
311A ALA* 4.0 9.2 - - + -
335A VAL* 3.7 18.4 - - + -
336A ARG* 1.3 74.3 - - - +
338A SER* 1.3 62.9 + - - +
340A PHE* 3.9 4.8 - - + -
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Residues in contact with SER 338 (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 LYS 3.5 18.2 - - - -
244A SER* 4.2 6.7 - - - -
281A PRO* 3.6 2.8 - - - +
282A LYS 3.2 5.0 + - - -
283A ALA* 3.1 38.7 + - - +
285A HIS* 4.6 9.0 + - - -
336A ARG 5.0 0.2 + - - -
337A PHE* 1.3 78.5 - - - +
339A LYS* 1.3 72.8 + - - +
340A PHE* 3.5 9.3 - - - -
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Residues in contact with LYS 339 (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 LYS 4.3 3.6 + - - -
282A LYS* 2.7 54.5 + - + +
283A ALA* 3.5 20.9 - - + +
301A THR* 4.5 14.6 - - + +
338A SER* 1.3 82.8 - - - +
340A PHE* 1.3 62.8 + - - +
5C A 4.3 18.4 + - + +
6C T 6.0 7.6 - - + +
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Residues in contact with PHE 340 (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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242A ARG 3.6 25.8 - - - -
243A LYS* 3.8 13.0 - - - -
245A ILE* 4.1 17.7 - - + -
276A LEU* 3.4 31.4 - - + -
279A ARG* 4.2 31.6 - - + -
280A ILE 3.4 4.7 - - - +
281A PRO* 3.8 21.8 - - + -
282A LYS* 3.8 5.5 + - - -
337A PHE 3.9 14.8 - - - -
338A SER* 4.0 14.1 - - - -
339A LYS* 1.3 80.3 - - - +
341A ILE* 1.3 67.5 + - - +
342A GLU* 3.4 3.1 + - - +
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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