Contacts of the strand formed by residues 500 - 504 (chain A) in PDB entry 4Z4Q
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 LYS 500 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A LYS 5.6 0.6 + - - -
427A ASN 3.8 1.2 + - - -
428A GLU* 3.4 37.1 + - + +
429A LEU 3.0 23.6 + - - -
498A TYR* 3.5 3.0 - - - +
499A ASP* 1.3 102.9 + - - +
501A ILE* 1.3 63.7 + - - +
502A ILE* 3.9 8.2 + - + -
534A HIS 3.4 5.4 - - - -
536A TYR* 3.2 39.7 - - + +
598A PRO* 6.2 0.2 - - - +
601A ARG* 4.1 13.9 - - - +
603A LEU* 5.4 1.6 - - + -
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Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 3.5 24.5 - - + +
431A LEU* 4.2 22.2 - - + -
483A ILE* 3.2 37.2 - - + -
498A TYR* 4.5 11.9 - - + +
500A LYS* 1.3 77.7 - - - +
502A ILE* 1.3 61.0 + - - +
503A ILE* 4.1 0.7 - - + -
522A PHE* 4.3 13.7 - - + -
529A LEU* 3.6 24.5 - - + -
534A HIS* 2.5 18.3 + - + +
535A VAL* 3.4 10.8 - - + +
536A TYR* 2.8 26.7 + - - +
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Residues in contact with ILE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 3.5 19.7 - - + +
429A LEU 2.7 13.0 + - - +
430A TYR* 3.3 55.2 - - + +
431A LEU* 2.8 25.3 + - - -
500A LYS* 4.1 17.7 - - + +
501A ILE* 1.3 76.3 - - - +
503A ILE* 1.3 62.6 + - - +
504A MET 3.7 0.9 + - - -
536A TYR* 3.9 10.1 - - + -
538A ALA* 3.9 25.8 - - + +
601A ARG* 3.6 11.2 - - - +
603A LEU* 4.2 15.5 - - + -
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 3.6 27.8 - - + +
501A ILE 5.1 0.9 - - - +
502A ILE* 1.3 71.0 - - - +
504A MET* 1.3 61.6 + - - +
505A THR* 4.2 15.1 + - + -
515A GLN* 4.5 15.9 + - + +
518A LEU* 3.5 42.0 - - + -
519A LEU* 4.4 13.7 - - + -
522A PHE* 4.3 6.1 - - + -
535A VAL* 4.1 23.6 - - + -
536A TYR 3.2 13.1 + - - +
537A ILE* 3.5 13.4 - - + +
538A ALA 3.0 23.3 + - - +
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Residues in contact with MET 504 (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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430A TYR* 4.1 28.0 - - + -
431A LEU 2.8 12.3 + - - +
432A VAL* 3.4 41.7 - - + -
433A GLU 3.1 22.3 + - - -
441A ALA* 4.2 12.6 - - + -
503A ILE* 1.3 75.7 - - - +
505A THR* 1.3 61.0 + - - +
538A ALA* 3.8 20.0 - - + +
540A PRO* 4.9 1.3 - - + -
583A LEU* 3.8 19.4 - - + +
591A LEU* 3.8 24.9 - - + -
595A THR* 3.5 22.2 - - - +
596A MET* 4.3 3.8 - - - -
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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