Contacts of the strand formed by residues 311 - 318 (chain A) 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 VAL 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A GLY* 3.6 27.4 - - - -
306A GLY* 3.1 22.8 + - - +
307A LYS* 3.8 2.1 + - - -
309A HIS* 3.8 8.7 - - + +
310A GLY* 1.3 85.6 - - - +
312A PRO* 1.3 78.7 - - + +
314A LEU* 4.3 3.4 - - + -
345A ARG 5.5 1.0 - - - +
5C TRP* 3.6 42.6 - - + -
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Residues in contact with PRO 312 (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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304A THR 3.6 1.2 - - - +
306A GLY* 3.3 9.4 + - - -
311A VAL* 1.3 99.2 - - + +
313A ILE* 1.3 64.2 + - - +
314A LEU* 3.3 20.7 + - + +
335A ALA* 3.8 29.6 - - + -
336A ILE 5.3 2.5 - - - +
337A LEU* 5.5 6.5 - - + -
344A LEU 5.6 1.1 - - - +
345A ARG* 5.2 13.9 - - + +
370A VAL* 6.3 1.8 - - + -
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Residues in contact with ILE 313 (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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303A ILE* 3.9 37.2 - - + -
304A THR 3.6 2.5 - - - +
305A GLY 3.9 6.5 - - - +
306A GLY* 3.5 26.0 - - - +
312A PRO* 1.3 71.4 - - - +
314A LEU* 1.3 57.4 + - - +
335A ALA* 3.3 4.0 - - - -
336A ILE* 2.8 54.9 + - + +
344A LEU* 4.0 12.3 + - + +
347A THR* 3.8 16.6 - - - +
349A HIS* 4.1 7.2 - - - +
352A ALA* 3.5 30.5 - - + -
356A LEU* 4.5 3.1 - - + -
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Residues in contact with LEU 314 (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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303A ILE* 3.2 7.0 - - - -
304A THR* 2.9 44.5 + - + +
311A VAL* 4.3 9.4 - - + -
312A PRO* 3.5 23.3 - - + +
313A ILE* 1.3 72.3 - - - +
315A ILE* 1.3 66.2 + - - +
316A SER 3.3 0.3 + - - -
333A GLY* 4.0 17.9 - - - +
334A ASP 3.5 1.1 - - - -
335A ALA* 3.9 25.6 - - + -
370A VAL* 6.1 2.5 - - + -
5C TRP* 3.8 29.8 - - + -
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Residues in contact with ILE 315 (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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301A ILE* 4.4 14.1 - - + -
302A SER 3.5 6.1 - - - +
303A ILE* 4.6 0.7 - - - +
314A LEU* 1.3 71.9 - - - +
316A SER* 1.3 57.9 + - - +
317A GLU 3.5 26.0 - - - +
318A ILE* 3.7 16.4 - - + -
330A LEU* 4.2 29.2 - - + -
331A HIS 3.7 21.1 - - - +
332A VAL* 3.5 4.0 - - - +
333A GLY* 2.8 30.0 + - - -
334A ASP* 2.8 26.8 + - + +
336A ILE* 3.9 28.9 - - + -
367A VAL* 5.3 0.2 - - + -
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Residues in contact with SER 316 (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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302A SER* 2.8 28.3 + - - -
303A ILE 4.1 1.7 + - - -
304A THR* 4.0 21.8 - - - -
314A LEU 3.3 1.0 + - - -
315A ILE* 1.3 73.2 - - - +
317A GLU* 1.3 71.2 + - - +
332A VAL* 3.7 19.8 - - - +
7C THR* 4.0 12.7 - - - +
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Residues in contact with GLU 317 (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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301A ILE* 3.3 5.7 - - - -
302A SER* 3.0 37.0 + - - -
315A ILE* 3.5 9.1 - - - +
316A SER* 1.3 93.6 + - - +
318A ILE* 1.3 63.7 + - - +
319A HIS* 3.0 31.8 - - + +
332A VAL* 3.8 5.2 - - - -
7C THR* 6.0 0.8 - - - +
9C ILE* 5.3 1.0 - - - +
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Residues in contact with ILE 318 (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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300A GLY 3.7 2.0 - - - +
301A ILE* 3.6 24.7 - - + -
315A ILE* 3.7 13.7 - - + -
317A GLU* 1.3 73.5 - - - +
319A HIS* 1.3 65.0 + - - +
320A PRO* 3.7 5.2 - - - +
324A ALA* 4.0 7.6 - - + +
325A ASP* 3.6 41.7 - - + +
330A LEU* 3.7 29.8 - - + +
331A HIS* 4.1 0.7 - - - -
332A VAL* 3.9 24.5 - - + +
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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