Contacts of the strand formed by residues 361 - 368 (chain B) in PDB entry 4NMQ
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 GLY 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291B LEU 3.3 4.3 - - - +
292B LEU* 3.9 7.9 - - - -
293B LYS* 2.8 46.4 + - - +
295B ASP* 5.0 3.5 + - - -
360B ARG* 1.3 74.9 - - - +
362B GLU* 1.3 60.2 + - - -
363B ILE* 3.4 5.5 + - - +
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Residues in contact with GLU 362 (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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290B LEU* 3.8 45.5 - - + +
291B LEU 3.5 6.3 - - - +
292B LEU* 4.1 15.4 - - + +
340B ASN* 4.2 6.4 + - - +
360B ARG 3.5 4.6 + - - +
361B GLY* 1.3 69.1 - - - -
363B ILE* 1.3 60.2 + - - +
364B GLU 4.1 0.9 + - - -
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Residues in contact with ILE 363 (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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289B VAL 3.3 4.0 - - - +
290B LEU* 3.5 3.0 - - - -
291B LEU 2.7 37.8 + - - +
293B LYS* 3.9 17.7 - - + -
299B LEU* 3.9 18.8 - - + -
339B VAL* 3.4 30.1 - - + -
340B ASN* 3.7 11.4 - - - +
356B LEU 5.4 0.2 - - - +
359B GLN* 3.7 33.4 - - + +
360B ARG 3.6 10.3 - - - +
361B GLY 3.5 15.7 - - - +
362B GLU* 1.3 75.1 - - - +
364B GLU* 1.3 60.9 + - - +
365B PHE* 3.6 16.8 - - + -
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Residues in contact with GLU 364 (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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295A ASP* 4.2 1.9 - - - +
402A GOL 2.7 29.2 + - - +
288B LYS* 3.7 38.1 + - + +
289B VAL 3.4 6.3 - - - +
290B LEU* 3.9 11.0 - - + +
339B VAL* 3.3 5.9 - - - +
340B ASN* 2.8 48.5 + - - +
341B GLY* 4.8 10.6 + - - -
362B GLU 4.1 1.0 + - - -
363B ILE* 1.3 71.6 - - - +
365B PHE* 1.3 65.2 + - - +
366B GLU* 4.0 3.7 + - - +
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Residues in contact with PHE 365 (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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287B ARG 3.5 2.4 - - - +
288B LYS* 3.3 3.8 - - - -
289B VAL* 2.8 40.1 + - + +
291B LEU* 3.8 26.0 - - + -
299B LEU* 3.7 25.8 - - + -
301B ILE* 4.2 15.5 - - + -
330B LEU* 4.1 19.3 - - + -
336B ILE* 4.1 30.7 - - + -
338B ALA 3.7 2.9 - - - -
339B VAL* 4.5 2.0 - - + -
356B LEU* 3.8 24.2 - - + -
363B ILE* 3.6 32.8 - - + -
364B GLU* 1.3 76.0 - - - +
366B GLU* 1.3 60.1 + - - +
367B VAL* 3.7 12.5 + - + -
10D ILE* 4.8 0.7 - - + -
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Residues in contact with GLU 366 (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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298A GLY* 5.3 0.9 - - - -
357A SER* 4.2 16.0 + - - -
286B ILE* 3.6 32.7 - - + +
287B ARG 3.5 3.1 - - - -
288B LYS* 4.1 28.1 + - + -
336B ILE 3.6 0.2 - - - -
337B LEU* 2.8 37.2 + - + +
338B ALA* 2.9 35.8 + - + +
341B GLY* 6.0 0.3 - - - -
345B ARG* 2.9 29.6 + - - -
364B GLU* 4.0 3.6 + - - +
365B PHE* 1.3 72.3 - - - +
367B VAL* 1.3 54.7 + - - +
10C ILE* 4.4 2.6 - - - -
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Residues in contact with VAL 367 (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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285B PRO 4.0 0.3 - - - +
286B ILE* 3.3 5.4 - - - +
287B ARG* 2.9 73.8 + - - +
289B VAL* 4.2 13.0 - - + -
315B ILE* 5.1 0.2 - - + -
330B LEU* 3.8 21.5 - - + -
334B ASP* 4.3 10.1 - - + -
335B ALA 3.1 13.9 - - - +
336B ILE* 4.1 16.2 - - + -
337B LEU* 4.6 2.9 - - - -
365B PHE* 4.0 11.0 - - + +
366B GLU* 1.3 80.1 - - - +
368B VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 368 (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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284B GLY 3.1 31.0 - - - +
285B PRO 3.9 8.1 - - - +
286B ILE* 4.1 6.7 - - + +
287B ARG* 3.8 6.5 - - - +
333B GLY 4.4 0.5 - - - +
334B ASP* 3.9 0.7 - - - -
335B ALA* 2.9 36.0 + - + +
337B LEU* 3.9 32.8 - - + -
367B VAL* 1.3 75.6 - - - +
369B TYR* 1.3 66.6 - - - +
9C ILE* 5.0 18.4 - - + -
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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