Contacts of the strand formed by residues 599 - 606 (chain C) in PDB entry 1ZYC
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 PHE 599 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594C ARG* 4.8 4.5 - - + -
595C TYR* 3.0 43.4 + + + +
596C ALA* 4.2 7.8 - - - +
598C ASP* 1.3 100.0 - - + +
600C GLU* 1.3 61.4 + - - +
601C GLU 3.8 1.8 + - - -
616C ALA* 3.9 13.7 - - + -
617C ARG 3.1 4.5 - - - +
618C ASN* 4.1 23.1 - - + -
619C ALA* 5.3 1.8 - - - -
625C TYR* 4.1 15.0 - + - -
627C ILE* 3.5 22.4 - - + -
662C TRP* 3.9 23.6 - + - -
787C GLN* 3.0 37.0 - - + -
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Residues in contact with GLU 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C PHE* 1.3 71.7 - - - +
601C GLU* 1.3 68.4 + - - +
602C ILE* 3.4 13.2 + - - +
616C ALA* 4.5 0.7 - - - -
617C ARG* 2.6 69.8 + - + +
619C ALA* 5.8 2.4 - - + +
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Residues in contact with GLU 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595C TYR* 2.7 35.4 + - + +
599C PHE 3.8 3.6 + - - -
600C GLU* 1.3 76.7 - - - +
602C ILE* 1.3 73.7 + - - +
603C ALA* 4.8 2.0 - - - +
604C VAL* 5.7 2.7 - - - +
614C VAL* 2.8 30.8 - - + +
615C LYS 4.1 2.7 - - - -
616C ALA* 4.5 1.3 - - - -
629C LYS* 3.5 12.9 + - - -
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Residues in contact with ILE 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600C GLU* 3.9 27.1 - - - +
601C GLU* 1.3 85.9 - - - +
603C ALA* 1.3 69.4 + - + +
615C LYS* 2.8 34.7 + - + +
617C ARG* 4.2 8.7 - - + +
624C TYR* 3.9 30.7 - - + +
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Residues in contact with ALA 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C GLU* 5.4 1.8 - - - -
602C ILE* 1.3 90.4 - - + +
604C VAL* 1.3 69.8 + - - +
605C LEU* 6.1 0.7 - - + -
614C VAL* 3.6 3.8 - - - +
615C LYS* 2.8 31.4 + - + +
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Residues in contact with VAL 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C GLU* 5.7 3.1 - - - +
603C ALA* 1.3 80.5 - - - +
605C LEU* 1.3 69.9 + - - +
606C GLY* 3.7 21.5 - - - +
607C GLN* 4.7 2.9 - - + +
612C GLN* 2.8 32.1 - - - +
613C VAL 4.1 4.0 - - - +
614C VAL* 4.3 7.9 - - + -
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Residues in contact with LEU 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603C ALA* 6.3 0.4 - - + -
604C VAL* 1.3 81.2 - - - +
606C GLY* 1.3 56.7 + - - +
613C VAL* 2.8 26.9 + - + +
614C VAL 4.2 3.1 - - - -
615C LYS* 3.8 35.2 - - + +
626C ALA* 4.4 13.7 - - + -
790C TYR* 3.9 28.0 - - + +
791C CYS 6.0 0.7 - - - +
793C ASN* 5.8 9.2 - - + -
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Residues in contact with GLY 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C VAL* 3.7 5.6 - - - +
605C LEU* 1.3 81.4 - - - +
607C GLN* 1.3 66.1 + - - -
612C GLN* 2.9 24.9 - - - +
613C VAL* 3.0 16.0 + - - +
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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