Contacts of the strand formed by residues 311 - 319 (chain A) in PDB entry 5I2S
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 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A TYR 3.9 9.9 + - - -
262A PRO* 3.2 16.4 - - - -
264A GLN* 4.0 1.6 + - - -
310A PRO* 1.3 75.6 - - - +
312A THR* 1.3 69.7 + - - +
329A ARG* 4.1 4.7 - - - -
330A TYR* 2.8 37.5 + - - +
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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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23A TYR* 5.3 0.2 + - - -
135A LEU* 3.9 11.0 - - + -
144A VAL* 3.9 26.9 - - + +
261A ALA* 4.6 10.9 + - + +
262A PRO 3.0 8.7 + - - +
263A SER* 3.1 23.6 - - - -
264A GLN* 3.3 24.6 + - - -
311A GLY* 1.3 76.6 - - - +
313A GLY* 1.3 59.1 + - - +
327A GLU* 3.9 1.2 + - - -
328A THR 3.2 8.3 - - - -
329A ARG* 3.8 35.0 - - + +
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Residues in contact with GLY 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 5.2 1.6 - - - -
264A GLN* 4.1 9.0 - - - -
311A GLY 3.7 0.2 + - - -
312A THR* 1.3 75.2 - - - +
314A PRO* 1.3 78.1 - - - +
327A GLU* 3.0 15.2 + - - -
328A THR* 2.9 32.6 + - - +
330A TYR* 3.8 7.6 - - - -
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Residues in contact with PRO 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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21A TYR* 3.4 17.7 - - - +
23A TYR* 3.5 36.6 - - + -
146A SER* 3.3 15.7 - - - +
307A PRO* 3.2 22.7 - - + +
313A GLY* 1.3 84.5 - - - +
315A ALA* 1.3 53.2 + - - +
316A PHE* 3.4 25.0 - - + -
325A TYR* 3.9 9.2 - - + -
326A PHE 3.5 7.2 - - - +
327A GLU* 3.3 4.6 - - - +
330A TYR* 2.5 22.3 + - - -
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Residues in contact with ALA 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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7A PRO* 4.5 8.5 - - + -
14A TRP* 3.3 8.5 - - + -
314A PRO* 1.3 73.4 - - - +
316A PHE* 1.3 62.8 + - - +
325A TYR* 2.8 26.3 - - - +
326A PHE* 2.9 36.2 + - + -
328A THR* 3.9 11.0 - - + -
330A TYR* 3.3 15.5 - - + +
370A PRO* 4.6 2.9 - - + -
371A ASN* 3.7 4.7 - - - +
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Residues in contact with PHE 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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14A TRP* 3.8 1.8 - - - -
17A VAL* 4.4 5.6 - - + -
21A TYR* 3.7 26.5 - + - -
23A TYR* 4.7 3.8 - - + -
288A TRP* 4.2 14.1 - + - -
302A LEU* 4.3 19.5 - - + +
305A LEU* 3.7 43.5 - - + -
314A PRO* 3.4 34.5 - - + -
315A ALA* 1.3 74.3 - - - +
317A THR* 1.3 62.8 + - - +
323A LEU* 4.6 4.7 - - + -
324A LYS 3.1 8.7 - - - +
325A TYR* 3.5 27.4 - - + -
370A PRO* 3.5 1.7 - - - +
371A ASN* 2.6 49.4 + - - +
372A GLY 4.4 0.3 + - - -
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Residues in contact with THR 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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14A TRP* 3.5 39.9 - - + -
302A LEU* 4.2 7.9 - - - -
316A PHE* 1.3 75.6 - - - +
318A ILE* 1.3 68.0 + - - +
319A ILE* 3.6 21.6 - - + +
323A LEU* 3.6 7.2 - - - +
324A LYS* 2.9 32.4 + - + +
361A ALA* 5.4 0.6 - - + +
368A ILE* 3.6 14.6 + - - +
369A GLY* 2.7 24.9 + - - -
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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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297A ILE* 3.7 25.4 - - + +
298A SER 5.9 0.4 - - - +
302A LEU* 4.0 16.4 - - + +
317A THR* 1.3 82.4 + - - +
319A ILE* 1.3 63.8 + - - +
320A ASN 3.7 16.0 - - - +
322A THR 3.3 11.7 - - - +
323A LEU* 4.6 1.3 - - + -
361A ALA* 4.4 0.7 - - - +
362A PRO 4.0 9.7 - - - +
363A TYR* 3.9 29.1 - - + +
368A ILE* 3.7 19.8 - - + +
400A SER* 3.7 19.7 - - - +
401A LYS 4.0 8.1 - - - +
402A ALA* 3.6 24.9 - - + -
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Residues in contact with ILE 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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14A TRP* 3.4 43.1 - - + +
317A THR* 3.6 13.8 + - + -
318A ILE* 1.3 76.0 - - - +
320A ASN* 1.3 74.7 + - + +
321A GLY 3.1 0.5 + - - -
322A THR* 2.9 26.3 + - - +
324A LYS* 4.1 18.1 - - + +
359A ASP* 5.6 0.2 - - - +
361A ALA* 3.9 24.0 - - + -
362A PRO* 5.1 2.2 - - + -
503A NAG 5.7 7.6 - - - -
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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