Contacts of the strand formed by residues 496 - 501 (chain B) in PDB entry 3GEB
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 VAL 496 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B GLU 3.3 7.4 + - - +
269B ARG* 3.1 26.8 - - + +
270B VAL 2.7 31.2 + - - +
494B LYS 5.0 3.8 - - - +
495B ALA* 1.3 74.7 - - - +
497B TYR* 1.3 57.5 + - - +
498B VAL* 3.8 4.6 + - + -
516B PRO* 4.3 13.2 - - + -
267C MET* 3.2 37.5 - - + -
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Residues in contact with TYR 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.3 29.8 - - + +
272B VAL* 4.7 6.5 - - + -
487B ILE* 3.6 30.7 - - + -
488B MET* 3.0 41.6 + - + -
491B PHE* 2.8 28.7 - + - +
492B GLY 2.9 24.8 + - - -
493B ARG* 5.1 0.9 - - - -
495B ALA* 3.2 26.5 - - + +
496B VAL* 1.3 73.4 - - - +
498B VAL* 1.3 61.6 + - - +
499B VAL 4.0 0.4 - - - -
515B MET* 3.3 41.8 - - + +
516B PRO* 3.4 11.3 - - - +
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Residues in contact with VAL 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ARG* 4.6 10.1 - - + +
270B VAL 2.8 11.5 + - - +
271B PHE* 3.5 32.4 - - + -
272B VAL* 2.8 27.6 + - - +
496B VAL* 4.3 13.9 - - + +
497B TYR* 1.3 73.9 - - - +
499B VAL* 1.3 64.0 + - - +
500B ILE* 3.6 11.3 + - + +
516B PRO* 3.7 20.2 - - + +
518B TRP* 4.2 24.5 - - + -
538B LEU* 4.4 15.5 - - + -
267C MET* 5.2 1.6 - - + -
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 3.5 18.6 - - + +
484B PHE* 4.2 17.7 - - + -
498B VAL* 1.3 73.4 - - - +
500B ILE* 1.3 62.6 + - - +
506B GLU* 3.7 23.6 - - + +
510B ALA* 3.8 19.1 - - + -
515B MET* 3.9 26.7 - - + -
516B PRO 3.0 8.0 + - - +
517B PHE* 3.0 30.6 - - + -
518B TRP 2.9 25.3 + - - -
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Residues in contact with ILE 500 (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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271B PHE* 4.0 25.4 - - + -
272B VAL 2.8 13.0 + - - +
273B TRP* 3.6 45.5 - - + -
274B ASP* 3.3 25.1 + - - +
278B THR* 3.8 2.9 - - + +
498B VAL* 4.1 14.4 - - + +
499B VAL* 1.3 77.9 - - - +
501B GLY* 1.3 56.6 + - - +
506B GLU* 5.3 0.4 - - - +
517B PHE* 4.4 0.4 - - - -
518B TRP* 3.7 11.7 - - + +
520B ILE* 3.3 33.4 - - + -
529B LEU* 3.6 20.9 - - + -
533B LEU* 6.1 0.7 - - + -
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Residues in contact with GLY 501 (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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274B ASP* 4.0 2.0 - - - -
278B THR* 3.9 11.2 - - - -
500B ILE* 1.3 76.3 - - - +
502B ASP* 1.3 60.6 + - - -
506B GLU* 3.2 16.4 - - - -
517B PHE* 3.0 30.1 - - - -
518B TRP 3.2 7.1 + - - +
519B ARG* 3.3 0.3 - - - -
520B ILE* 3.1 17.7 + - - -
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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
------------------------------------------------------------
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