Contacts of the strand formed by residues 601 - 605 (chain B) in PDB entry 5ZE3
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 SER 601 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B LEU* 4.2 9.3 - - - +
599B PHE* 2.9 21.7 - - - -
600B SER* 1.3 70.3 + - - +
602B GLN* 1.3 59.0 + - - +
603B ILE* 4.0 10.5 + - - +
636B THR* 5.7 0.2 - - - +
638B TYR* 2.9 22.0 + - - -
656B PHE* 4.3 6.1 - - - -
687B ASP 3.6 4.3 - - - +
688B MET* 4.2 0.9 - - - -
689B TYR* 2.9 36.3 + - - +
696B GLN* 3.3 19.5 - - - -
712B VAL* 4.9 1.7 - - - +
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Residues in contact with GLN 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B VAL 3.6 0.2 - - - +
552B LEU* 3.1 9.9 - - - +
553B ASN* 2.8 43.3 + - + +
556B MET* 3.1 36.4 - - + +
600B SER 4.1 1.6 + - - -
601B SER* 1.3 72.3 - - - +
603B ILE* 1.3 61.1 + - - +
604B HIS* 3.5 14.7 + - - -
686B TRP* 2.8 56.0 - - + +
687B ASP 3.5 1.1 - - - +
688B MET* 3.4 37.5 - - + +
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Residues in contact with ILE 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B LEU* 3.9 21.5 - - + -
551B VAL 3.6 2.5 - - - +
552B LEU* 4.3 4.0 - - + -
601B SER* 4.0 17.9 - - - +
602B GLN* 1.3 78.4 - - - +
604B HIS* 1.3 69.7 + - - +
635B PHE* 4.1 20.0 - - + -
636B THR* 5.1 1.8 - - + -
656B PHE* 4.4 12.8 - - + -
681B ILE* 3.8 22.9 - - + +
686B TRP* 3.0 7.1 - - - -
687B ASP* 2.8 41.5 + - + +
714B ILE* 3.3 36.6 - - + -
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Residues in contact with HIS 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ILE* 4.6 12.7 - - + +
549B ASP 3.4 0.3 - - - +
550B LEU* 2.8 37.2 - - - +
551B VAL* 2.9 23.9 + - + +
553B ASN* 3.2 40.7 + - + +
602B GLN* 3.5 12.9 + - - -
603B ILE* 1.3 79.9 - - - +
605B ASN* 1.3 53.5 + - - +
606B ASN* 3.7 29.4 + - - +
664B GLU* 5.5 6.6 + - - -
685B CYS 3.6 4.9 + - - +
686B TRP* 3.6 30.5 - + + -
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Residues in contact with ASN 605 (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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548B PRO* 3.3 7.4 - - - +
549B ASP 3.1 25.9 + - - -
550B LEU* 3.8 9.2 - - + -
603B ILE 4.2 0.6 + - - -
604B HIS* 1.3 70.5 - - - +
606B ASN* 1.3 58.8 + - - +
607B GLY 3.2 5.1 + - - -
609B SER 2.8 24.0 + - - +
611B PHE 3.2 5.3 - - - +
681B ILE* 2.9 33.5 + - + +
682B THR 3.3 20.4 + - - +
683B MET* 3.7 2.4 - - - +
684B GLY* 2.9 33.8 + - - -
685B CYS 3.0 9.6 + - - +
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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