Contacts of the strand formed by residues 601 - 605 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552A LEU* 4.0 13.3 - - - +
557A VAL* 5.4 0.2 - - - -
599A PHE* 3.4 13.6 + - - -
600A SER* 1.3 68.7 - - - +
602A GLN* 1.3 59.5 + - - +
603A ILE* 3.5 20.1 - - - +
636A THR* 5.7 0.2 - - - -
638A TYR* 2.6 37.0 + - - -
656A PHE* 4.4 3.4 - - - -
687A ASP 3.5 4.5 - - - +
688A MET* 4.3 0.9 - - - -
689A TYR* 2.9 33.1 + - - +
696A GLN* 3.5 5.3 + - - -
712A VAL* 5.3 0.2 - - - +
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Residues in contact with GLN 602 (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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552A LEU* 4.0 3.8 - - - +
553A ASN* 2.9 42.0 + - + +
556A MET* 3.6 22.8 - - + +
600A SER 3.8 3.4 + - - -
601A SER* 1.3 73.3 - - - +
603A ILE* 1.3 58.7 + - - +
604A HIS* 3.3 29.1 + - - +
686A TRP* 3.0 46.6 + - + +
687A ASP 3.5 3.6 - - - -
688A MET* 3.1 33.2 - - + +
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Residues in contact with ILE 603 (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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550A LEU* 4.0 23.3 - - + -
551A VAL 3.3 7.6 - - - +
552A LEU* 3.8 5.2 - - + -
601A SER* 3.5 35.0 - - - +
602A GLN* 1.3 72.1 - - - +
604A HIS* 1.3 73.5 + - - +
635A PHE* 4.2 12.6 - - + -
636A THR* 5.2 2.9 - - + -
656A PHE* 4.3 17.5 - - + -
681A ILE* 4.2 11.2 - - + +
686A TRP* 3.1 1.8 - - - -
687A ASP* 2.8 41.8 + - + +
714A ILE* 3.3 32.3 - - + -
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Residues in contact with HIS 604 (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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385A ILE* 4.4 18.1 - - + +
549A ASP 3.5 0.5 - - - +
550A LEU* 3.1 12.1 - - - +
551A VAL* 2.7 46.3 + - + +
552A LEU 4.8 0.4 - - - -
553A ASN* 3.1 34.3 + - + +
602A GLN* 3.3 35.4 + - + -
603A ILE* 1.3 75.9 - - - +
605A ASN* 1.3 59.6 + - - +
606A ASN* 3.7 18.2 + - - +
664A GLU* 4.8 7.4 + - - -
681A ILE* 4.9 0.2 - - - -
685A CYS 3.6 5.8 - - - +
686A TRP* 3.9 27.1 - + + -
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Residues in contact with ASN 605 (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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548A PRO* 3.5 7.4 - - - +
549A ASP 3.1 26.1 + - - -
550A LEU* 4.2 4.4 - - + +
603A ILE 4.1 0.2 + - - -
604A HIS* 1.3 70.7 - - - +
606A ASN* 1.3 62.4 + - - +
607A GLY 3.4 3.2 + - - -
609A SER 2.9 21.8 + - - +
611A PHE* 3.3 6.5 - - - +
681A ILE* 2.8 37.2 + - + +
682A THR 3.3 12.1 - - - +
683A MET* 3.0 15.5 - - - +
684A GLY* 2.8 32.1 + - - -
685A CYS 2.8 10.3 + - - +
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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