Contacts of the strand formed by residues 311 - 316 (chain A) in PDB entry 3NN9
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 THR 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A TYR* 3.4 6.5 + - - -
264A LYS* 5.1 3.1 - - - +
266A GLU* 3.6 19.7 - - - +
305A ILE* 3.5 0.3 - - - -
306A ASP* 2.9 30.6 + - - +
309A ALA* 3.5 23.1 + - - +
310A MET* 1.3 74.3 - - - +
312A HIS* 1.3 68.9 + - - +
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Residues in contact with HIS 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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254A ILE* 4.0 15.2 - - + +
256A TYR* 4.1 6.7 + - - +
266A GLU* 3.0 29.8 + - + +
267A PRO 3.3 24.7 - - - -
268A LEU* 3.6 8.9 - - + +
269A ALA* 3.0 41.6 + - + +
303A ILE* 3.8 23.8 - - + -
304A ARG 3.1 14.1 - - - +
305A ILE* 4.1 6.3 - - + -
311A THR* 1.3 85.4 - - - +
313A THR* 1.3 71.4 + - - +
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Residues in contact with THR 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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269A ALA 4.0 7.0 - - - -
270A GLY* 5.1 2.0 - - - -
303A ILE* 3.1 7.8 - - - +
304A ARG* 2.9 43.8 + - - +
312A HIS* 1.3 82.7 - - - +
314A SER* 1.4 63.1 + - - +
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Residues in contact with SER 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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268A LEU* 4.3 11.6 - - - +
269A ALA 2.9 23.1 + - - -
270A GLY* 3.3 3.5 - - - -
271A THR* 3.1 20.0 + - - -
272A ALA* 2.9 34.9 + - - +
302A VAL 3.0 12.6 - - - -
303A ILE* 4.5 4.3 - - - -
313A THR* 1.4 78.7 - - - +
315A GLN* 1.3 63.9 + - - +
338A ASN* 5.0 0.2 + - - -
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Residues in contact with GLN 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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271A THR* 3.7 7.6 - - - -
272A ALA* 4.3 3.6 - - - +
301A PRO* 3.3 7.8 - - - +
302A VAL* 2.9 26.7 + - + +
314A SER* 1.3 75.4 - - - +
316A TYR* 1.3 88.0 + - - +
318A CYS* 3.8 9.3 - - - -
337A CYS* 3.4 12.4 + - - +
338A ASN* 3.7 15.0 - - - +
383A LEU* 3.1 40.5 + - + +
384A THR* 5.1 4.6 - - - +
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Residues in contact with TYR 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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271A THR 3.6 21.3 - - - -
272A ALA* 3.7 7.0 - - - -
273A LYS* 3.0 23.7 + - - +
274A HIS 4.3 0.2 + - - -
293A ASP* 2.7 28.8 + - - -
297A GLY* 4.9 0.2 - - - -
299A ASN* 3.5 41.5 - - - +
300A ARG 3.4 5.2 - - - -
301A PRO* 3.8 26.9 - - + -
302A VAL* 4.9 1.1 - - - -
315A GLN* 1.3 103.7 + - - +
317A ILE* 1.3 64.0 + - - +
336A LYS 3.8 3.1 - - - +
337A CYS 3.0 15.0 + - - +
338A ASN* 3.9 4.0 - - - -
339A ASP 3.8 16.8 - - - -
340A PRO* 3.6 22.0 - - + +
383A LEU* 4.1 2.6 - - - +
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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