Contacts of the strand formed by residues 490 - 495 (chain B) in PDB entry 4ICU
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 LEU 490 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B LYS* 4.9 1.3 - - - +
487B SER 5.8 2.2 - - - +
488B ASP 4.3 7.9 - - - +
489B LEU* 1.3 78.8 - - - +
491B LEU* 1.3 63.1 + - - +
492B SER* 5.7 0.2 - - - -
524B LEU 3.7 2.9 - - - +
526B ARG* 2.7 61.4 + - + +
527B TRP* 5.0 5.4 - - - +
507C ASN* 5.5 6.7 - - - +
510C LYS* 5.2 15.0 - - - +
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ILE* 4.2 12.8 - - + +
474B VAL* 3.8 31.9 - - + -
475B LYS* 3.8 34.0 - - + +
478B LEU* 3.8 21.3 - - + -
489B LEU* 4.1 4.8 + - + -
490B LEU* 1.3 81.9 - - - +
492B SER* 1.3 62.3 + - - +
504B GLU* 4.2 1.6 - - - +
505B LEU* 3.1 44.7 + - + +
512B LEU* 6.5 0.2 - - + -
523B LEU* 4.8 6.3 - - + -
524B LEU 3.6 1.8 - - - +
525B VAL* 3.8 22.4 - - + -
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Residues in contact with SER 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B LEU* 1.3 76.6 - - - +
493B TYR* 1.3 65.0 + - - +
502B GLU* 2.7 32.1 + - - -
503B ILE 3.2 22.0 - - - -
504B GLU* 4.1 6.7 - - - -
505B LEU* 4.1 6.3 - - - -
523B LEU* 3.7 6.4 - - - +
524B LEU* 2.8 38.6 + - - +
526B ARG* 4.0 3.6 + - - -
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Residues in contact with TYR 493 (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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454A HIS* 4.3 6.9 - - - +
492B SER* 1.3 76.6 - - - +
494B GLU* 1.3 66.8 + - - +
495B SER* 4.6 8.3 - - - -
498B LYS* 4.6 5.4 + - - -
501B ARG 3.5 2.6 - - - +
502B GLU* 3.6 0.5 - - - -
503B ILE* 2.8 71.4 + - + +
505B LEU* 3.7 16.4 - - + -
515B TYR 2.6 30.1 + - - -
516B SER* 3.2 13.1 + - - -
517B VAL* 3.6 28.0 - - + -
521B ASP* 3.5 28.7 - - + -
522B CYS 3.2 14.4 - - - +
523B LEU* 4.4 11.4 - - + -
524B LEU* 3.8 5.6 - - - -
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Residues in contact with GLU 494 (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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451B LYS* 4.1 16.6 + - - -
459B LYS* 5.9 0.7 - - - -
493B TYR* 1.3 78.4 - - - +
495B SER* 1.3 64.1 + - - +
496B PRO* 4.2 1.0 - - - +
498B LYS 5.2 0.4 - - - +
499B PRO* 6.1 0.2 - - + -
500B GLY* 5.3 9.5 - - - +
501B ARG 3.4 22.0 + - - +
502B GLU* 3.9 12.1 - - - +
503B ILE* 4.9 0.7 - - - -
521B ASP* 3.6 2.4 - - - +
522B CYS* 2.9 51.5 + - + +
524B LEU* 3.7 28.4 - - + +
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Residues in contact with SER 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B TYR* 4.5 5.3 - - - -
494B GLU* 1.3 75.9 - - - +
496B PRO* 1.4 67.2 - - - +
497B LYS* 3.1 29.4 + - - +
498B LYS* 3.1 47.6 + - - +
499B PRO* 3.6 3.8 - - - +
501B ARG 4.9 0.2 + - - -
503B ILE* 5.2 2.4 - - - +
518B GLU* 4.9 3.0 + - - -
521B ASP* 3.4 21.7 + - - -
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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
------------------------------------------------------------
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