Contacts of the strand formed by residues 476 - 480 (chain A) in PDB entry 4X8G
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 476 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A GLU* 5.1 14.9 - - + +
429A LEU* 4.4 10.3 - - + -
462A LEU* 3.8 22.4 - - + -
472A VAL* 3.2 28.0 + - + +
473A ASP* 3.3 20.5 + - - +
475A PHE* 1.3 104.0 - - + +
477A SER* 1.3 68.0 + - - +
478A PHE* 4.0 25.1 - - + -
489A LEU* 4.5 6.3 - - + -
490A LEU 3.2 9.0 - - - +
491A LEU* 3.8 13.9 - - + -
553A LEU* 4.7 5.4 - - + -
587A VAL* 4.0 4.1 - - - +
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Residues in contact with SER 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASN* 3.7 13.3 + - - +
476A LEU* 1.3 83.4 - - - +
478A PHE* 1.3 75.0 + - - +
489A LEU* 3.4 6.2 - - - +
490A LEU* 2.6 46.1 + - - +
587A VAL* 3.2 28.7 + - - -
588A ASN* 5.1 1.6 - - - -
589A MET* 4.7 10.9 + - - +
591A VAL* 4.7 1.9 - - - +
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Residues in contact with PHE 478 (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 PRO* 6.1 0.2 - - + -
301A ASN* 3.3 39.4 + - + +
302A THR* 5.0 2.9 - - + -
411A GLU* 5.8 3.6 - - + -
412A VAL 4.2 10.1 - - - -
413A SER* 3.9 25.6 - - - -
414A PRO* 3.5 33.4 - - + -
429A LEU* 4.0 13.2 - - + -
476A LEU* 4.0 20.4 - - + -
477A SER* 1.3 81.9 + - - +
479A VAL* 1.3 67.9 + - - +
487A PHE* 3.8 17.3 - + + -
488A ARG 3.4 13.5 - - - -
489A LEU* 3.6 26.2 - - + -
553A LEU* 5.6 0.7 - - + -
557A LEU* 4.2 11.9 - - + -
559A LEU* 5.2 0.4 - - + -
591A VAL* 3.9 3.1 - - - +
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 4.5 2.7 - - - -
477A SER* 5.2 0.7 - - - +
478A PHE* 1.3 81.3 - - - +
480A PRO* 1.3 68.7 - - + +
487A PHE* 3.2 6.1 - - - +
488A ARG* 2.9 50.3 + - + -
490A LEU* 3.6 35.7 - - + -
589A MET* 4.8 0.9 - - - -
591A VAL* 4.2 6.7 - - + -
596A LEU* 3.9 26.9 - - + -
620A LEU* 4.6 0.7 - - + -
623A LEU* 4.3 6.1 - - + -
625A LEU* 4.0 19.3 - - + -
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Residues in contact with PRO 480 (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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301A ASN 4.3 5.8 - - - +
302A THR* 4.1 30.3 - - + +
478A PHE 4.6 0.2 - - - +
479A VAL* 1.3 87.7 - - + +
481A ALA* 1.3 60.2 + - - +
482A PRO* 4.6 0.9 - - - +
486A GLY 3.6 7.0 - - - +
487A PHE* 4.4 0.4 - - - -
591A VAL* 3.8 17.3 - - + -
593A GLY* 3.6 27.1 - - - +
594A LYS* 4.0 14.9 + - + +
623A LEU* 4.6 1.2 - - - +
625A LEU* 3.5 27.2 - - + +
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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