Contacts of the strand formed by residues 292 - 302 (chain A) in PDB entry 4IRQ
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 TYR 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A VAL* 3.5 38.6 - - + -
150A LEU* 3.8 20.5 - - + +
151A GLU* 2.6 32.6 + - - +
290A VAL* 3.6 28.3 - - + -
291A LYS* 1.3 74.4 - - - +
293A HIS* 1.3 79.2 + - - +
294A VAL* 4.0 9.2 - - + -
312A ILE* 4.4 2.0 - - + -
313A MET 3.1 15.5 - - - +
314A LEU* 3.9 16.8 - - + -
315A ASP* 4.2 3.5 - - - +
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Residues in contact with HIS 293 (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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292A TYR* 1.3 88.6 - - - +
294A VAL* 1.3 81.0 + - - +
295A ALA* 3.5 13.2 + - - +
312A ILE* 3.9 0.7 - - - -
313A MET* 2.9 65.2 + - + +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 3.7 36.3 - - + -
292A TYR* 4.0 8.3 - - + -
293A HIS* 1.3 83.9 - - - +
295A ALA* 1.3 60.9 + - - +
296A SER 3.2 27.8 - - - +
297A ARG* 3.8 26.5 - - - +
310A LEU* 4.5 8.7 - - + -
311A ASN 3.3 12.6 - - - +
312A ILE* 4.7 8.5 - - + +
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Residues in contact with ALA 295 (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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134A VAL* 4.7 4.0 - - + -
293A HIS* 3.5 12.5 + - - +
294A VAL* 1.3 74.4 - - - +
296A SER* 1.3 60.9 + - - +
311A ASN* 2.7 24.0 + - + +
313A MET* 4.2 20.9 - - + -
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Residues in contact with SER 296 (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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294A VAL* 3.2 11.4 - - - +
295A ALA* 1.3 81.7 - - - +
297A ARG* 1.3 64.6 + - - +
298A THR* 5.0 5.5 - - - +
311A ASN* 2.8 55.2 + - - +
109D LEU* 5.5 0.2 - - - +
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Residues in contact with ARG 297 (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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129A TYR* 6.2 0.4 - - - -
151A GLU* 3.2 40.0 + - - -
294A VAL* 3.8 20.9 - - - +
296A SER* 1.3 76.7 - - - +
298A THR* 1.3 62.1 + - - +
308A THR* 4.1 12.3 - - + -
309A VAL 3.4 4.0 - - - -
310A LEU* 3.5 34.5 - - + +
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Residues in contact with THR 298 (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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296A SER* 5.0 7.2 - - - +
297A ARG* 1.3 76.3 - - - +
299A ALA* 1.3 73.5 + - - +
300A LEU* 3.4 1.5 + - + +
308A THR* 3.8 4.1 - - - -
309A VAL* 2.9 50.3 + - + +
311A ASN* 5.3 0.2 - - - +
109D LEU* 3.5 36.3 + - + +
302D VAL* 4.2 10.2 - - - +
303D GLY* 4.1 9.9 + - - -
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Residues in contact with ALA 299 (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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298A THR* 1.3 75.0 + - - +
300A LEU* 1.3 59.3 + - - +
307A CYS 3.8 7.0 - - - +
308A THR* 4.9 3.8 - - - +
301D SER 4.0 0.2 - - - +
302D VAL* 3.9 0.9 - - - -
303D GLY* 2.9 37.8 + - - +
304D GLY 4.7 0.4 + - - +
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Residues in contact with LEU 300 (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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108A LEU* 4.2 7.9 - - + -
298A THR* 3.4 1.7 + - - +
299A ALA* 1.3 76.0 - - - +
301A SER* 1.3 60.9 + - - +
302A VAL* 4.1 18.2 - - + -
306A PRO* 3.4 2.1 - - - +
307A CYS* 2.8 55.0 + - - +
309A VAL* 3.8 28.0 - - + -
105D PHE* 4.2 17.3 - - + -
109D LEU* 4.4 8.7 - - + -
300D LEU* 4.3 11.2 - - + -
301D SER 3.2 15.3 - - - +
302D VAL* 3.5 28.5 - - + -
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Residues in contact with SER 301 (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 LEU* 1.3 74.4 - - - +
302A VAL* 1.3 59.9 + - - +
303A GLY 3.9 0.6 + - - -
304A GLY* 3.3 31.8 + - - -
305A ALA 3.4 3.7 + - - -
306A PRO* 4.1 6.4 - - - +
300D LEU* 3.2 8.7 - - - +
301D SER* 2.8 51.0 + - - -
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Residues in contact with VAL 302 (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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108A LEU* 4.4 6.1 - - + +
109A LEU* 3.4 41.7 - - + +
112A VAL* 4.1 22.4 - - + -
113A PRO* 3.4 18.2 - - + +
300A LEU* 4.2 17.3 - - + -
301A SER* 1.3 76.2 - - - +
303A GLY* 1.3 68.5 - - - +
304A GLY 3.3 0.2 - - - -
305A ALA 2.6 21.6 + - - +
307A CYS* 4.8 2.0 - - - -
298D THR* 4.2 12.3 - - + -
300D LEU* 3.7 17.0 - - + -
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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