Contacts of the strand formed by residues 311 - 324 (chain A) in PDB entry 3F9B
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 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A GLU* 3.4 37.2 - - + +
271A PHE* 4.0 7.6 - - + -
272A ARG* 3.8 21.5 - - + +
275A ALA* 6.3 0.2 - - + -
307A THR* 3.3 2.8 - - - +
308A TYR* 2.7 41.3 + - + +
310A SER* 1.3 77.4 - - - +
312A THR* 1.3 63.2 + - - +
313A VAL* 3.9 13.5 - - + -
336A ILE* 3.5 29.4 - - + -
337A ARG 3.4 5.4 - - - +
338A GLU* 3.4 35.0 - - + +
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Residues in contact with THR 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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306A GLY 3.5 5.6 - - - +
307A THR* 3.1 25.7 + - - +
310A SER 4.0 2.7 + - - -
311A ILE* 1.3 73.7 - - - +
313A VAL* 1.3 67.0 + - - +
314A GLU* 6.1 0.2 - - + -
335A THR 3.5 2.3 - - - +
336A ILE* 3.6 1.2 - - - -
337A ARG* 2.8 70.1 + - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.7 53.4 - - + -
301A TYR 4.7 3.1 - - - +
304A GLN 5.0 3.1 - - - +
305A SER* 3.3 5.4 - - - -
306A GLY 2.8 38.5 + - - +
308A TYR* 4.1 10.3 - - + -
311A ILE* 3.9 10.1 - - + -
312A THR* 1.3 84.5 - - - +
314A GLU* 1.3 63.6 + - - +
315A SER 4.8 0.2 - - - +
334A LEU* 4.0 26.7 - - + -
335A THR 3.2 7.6 - - - +
336A ILE* 4.4 6.1 - - + -
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Residues in contact with GLU 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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305A SER* 3.4 9.4 - - - +
312A THR* 6.1 0.2 - - + -
313A VAL* 1.3 75.9 - - - +
315A SER* 1.3 66.4 + - - +
316A LYS* 3.8 30.2 + - + +
333A THR 3.4 2.3 - - - +
334A LEU* 3.4 2.9 - - - -
335A THR* 2.8 46.3 + - - +
337A ARG* 3.5 28.3 + - - +
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Residues in contact with SER 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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302A PHE 2.7 29.1 + - - -
303A ARG* 3.6 11.7 + - - -
304A GLN 3.7 24.7 - - - -
305A SER* 3.0 12.8 + - - -
313A VAL 4.2 0.4 - - - -
314A GLU* 1.3 75.6 - - - +
316A LYS* 1.3 64.2 + - - +
332A TYR* 3.9 9.5 - - - +
333A THR 3.5 4.8 + - - -
334A LEU* 3.9 5.6 - - - +
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Residues in contact with LYS 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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314A GLU* 3.8 33.6 + - + +
315A SER* 1.3 79.3 + - - +
317A MET* 1.3 66.0 + - - +
318A THR* 4.2 2.2 - - + +
332A TYR* 3.1 9.9 - - - +
333A THR* 2.9 48.1 + - - +
335A THR* 4.6 12.1 + - - -
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Residues in contact with MET 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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316A LYS* 1.3 75.0 - - - +
318A THR* 1.3 71.5 + - - +
331A MET 3.8 4.7 - - - +
332A TYR* 3.6 27.6 - - + +
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Residues in contact with THR 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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316A LYS* 3.7 5.8 + - + +
317A MET* 1.3 86.9 - - - +
319A GLN* 1.3 75.0 + - - +
331A MET* 2.9 36.2 + - - +
332A TYR* 3.4 2.6 + - - -
333A THR* 3.7 29.8 - - + +
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Residues in contact with GLN 319 (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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318A THR* 1.3 87.9 + - - +
320A GLN* 1.3 62.3 + - - +
321A VAL* 3.7 15.4 - - + +
330A ASP* 4.1 0.2 - - - -
331A MET* 2.9 66.2 + - + +
371A LEU* 5.5 1.6 - - - +
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Residues in contact with GLN 320 (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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319A GLN* 1.3 77.8 - - - +
321A VAL* 1.3 63.1 + - - +
322A GLY 4.3 0.7 + - - -
328A MET* 3.2 39.4 - - + +
329A ALA 3.3 4.9 - - - +
330A ASP* 2.9 27.4 + - - +
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Residues in contact with VAL 321 (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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319A GLN* 3.7 26.9 - - + +
320A GLN* 1.3 78.5 - - - +
322A GLY* 1.3 74.3 + - - +
323A LEU* 3.7 4.6 + - + +
328A MET* 4.2 2.7 - - - -
329A ALA* 2.9 38.2 + - - +
331A MET* 4.5 2.0 - - - -
371A LEU* 4.0 39.0 - - + -
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Residues in contact with GLY 322 (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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320A GLN 4.3 0.6 + - - -
321A VAL* 1.3 85.5 - - - +
323A LEU* 1.3 61.1 + - - +
324A GLY 3.6 2.5 - - - -
327A ILE 3.7 1.6 - - - -
328A MET* 3.7 25.1 - - - -
367A ALA* 5.3 1.6 - - - +
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Residues in contact with LEU 323 (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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321A VAL* 3.9 13.2 - - + +
322A GLY* 1.3 79.2 - - - +
324A GLY* 1.3 58.7 + - - +
327A ILE* 2.8 32.3 + - + +
329A ALA* 4.2 11.9 - - + +
351A VAL* 4.3 7.9 - - + -
363A GLU 4.3 1.0 - - - +
364A VAL* 3.6 27.8 + - + +
367A ALA* 3.5 29.7 - - + +
368A LEU* 3.9 48.0 - - + +
371A LEU* 4.2 17.5 - - + -
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Residues in contact with GLY 324 (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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322A GLY* 3.6 2.0 - - - -
323A LEU* 1.3 80.1 - - - +
325A ASP* 1.3 70.0 + - - +
326A GLY 3.1 3.1 - - - -
327A ILE* 2.9 26.8 + - - +
364A VAL* 3.6 5.3 - - - +
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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