Contacts of the strand formed by residues 493 - 498 (chain B) in PDB entry 2IAG
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 PRO 493 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B GLU* 5.3 3.8 - - - +
162B MET 3.8 6.5 - - - +
163B GLY* 4.4 3.1 - - - -
466B LEU* 4.0 1.9 - - - +
467B ILE* 3.3 39.8 + - + -
468B ASN* 4.8 3.8 + - + +
471B VAL* 5.0 11.6 - - + +
491B ASP 3.9 6.5 - - - +
492B VAL* 1.3 93.4 - - + +
494B VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B HIS 4.6 0.2 - - - -
161B GLU* 3.6 4.7 - - - +
162B MET* 2.7 55.2 + - + +
163B GLY 4.2 0.7 - - - +
164B LEU* 3.9 36.8 - - + -
167B PHE* 4.8 4.7 - - + -
300B LEU* 4.1 21.8 - - + -
464B LEU* 4.1 19.7 - - + -
465B GLU 3.4 15.7 - - - +
466B LEU* 4.2 5.6 - - + -
467B ILE* 3.8 10.4 - - - +
492B VAL* 4.2 0.9 - - + +
493B PRO* 1.3 80.1 - - - +
495B ARG* 1.3 63.6 + - - +
496B TYR* 5.7 0.7 - - + -
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Residues in contact with ARG 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TRP* 3.4 68.1 - - + +
160B HIS 3.5 6.7 - - - +
161B GLU* 4.7 7.2 - - + -
464B LEU* 3.5 3.5 - - - +
465B GLU* 2.9 59.6 + - + +
466B LEU 5.7 0.4 + - - -
467B ILE* 3.7 24.7 - - + +
494B VAL* 1.3 75.0 - - - +
496B TYR* 1.3 62.6 + - - +
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Residues in contact with TYR 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LEU* 4.3 7.4 - - + -
151B ASP* 5.0 3.6 + - - +
152B ALA* 4.2 27.0 + - + -
155B ALA* 5.3 2.1 - - - +
158B GLY 3.8 0.7 - - - +
159B TRP* 3.4 5.0 - - - -
160B HIS* 2.9 70.9 + - + +
162B MET* 4.0 28.0 - - + -
167B PHE* 3.7 29.6 - + + -
171B PHE* 4.3 13.1 - + - -
462B LEU* 4.0 13.5 - - + -
463B ASP 3.2 12.3 - - - +
464B LEU* 3.7 17.0 - - + -
494B VAL* 5.7 0.9 - - + -
495B ARG* 1.3 75.2 - - - +
497B ARG* 1.3 67.7 + - - +
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Residues in contact with ARG 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B SER 4.6 5.4 - - - +
158B GLY* 3.3 25.8 - - - +
159B TRP* 3.3 52.4 - - + +
160B HIS* 5.1 1.1 - - - -
462B LEU* 3.3 9.8 - - - +
463B ASP* 2.7 52.1 + - + +
496B TYR* 1.3 79.2 - - - +
498B ILE* 1.3 76.4 + - - +
500B PRO* 3.6 23.6 - - - +
502B HIS* 5.6 5.7 + - - -
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Residues in contact with ILE 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 4.8 19.1 - - + +
152B ALA* 3.6 23.1 - - + +
153B THR* 3.7 39.5 - - - +
156B GLY 4.6 7.6 - - - +
157B SER* 4.7 18.9 + - - +
158B GLY 4.9 0.8 + - - -
160B HIS* 5.9 0.8 - - + -
461B HIS* 4.1 7.2 - - + +
462B LEU* 3.9 12.7 - - + +
496B TYR* 5.0 0.8 - - - -
497B ARG* 1.3 81.5 - - - +
499B ARG* 1.3 75.9 + - + +
500B PRO* 3.2 8.7 - - - +
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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