Contacts of the strand formed by residues 593 - 598 (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 TYR 593 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A ASP* 4.0 33.9 - - + -
566A ARG 3.5 7.0 - - - -
567A PRO* 5.7 1.3 - - + -
568A MET* 4.7 0.4 - - - -
587A THR* 3.7 11.4 + - - +
591A THR 5.4 2.5 - - - -
592A GLY* 1.4 74.8 - - - -
594A ARG* 1.3 80.7 + - - +
595A ARG* 4.5 11.7 - - + +
701A THR* 4.5 11.7 - - + +
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Residues in contact with ARG 594 (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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564A GLU 3.4 1.7 - - - +
565A ASP* 3.0 3.4 - - - -
566A ARG 2.8 34.2 + - - -
568A MET* 3.8 20.6 - - - -
571A LEU* 3.6 23.6 - - + -
580A LEU* 4.0 7.4 - - + -
581A SER* 3.2 11.7 + - - -
583A SER* 2.8 24.0 + - - -
584A ALA* 3.0 35.5 - - - +
587A THR* 3.2 16.3 + - - -
593A TYR* 1.3 82.4 + - - +
595A ARG* 1.3 59.6 + - - +
596A LEU* 3.7 22.2 + - + +
699A ASP* 2.9 23.6 + - - -
701A THR* 3.2 29.5 + - - +
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Residues in contact with ARG 595 (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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563A LEU* 4.3 20.8 - - + +
564A GLU 3.5 6.3 - - - +
565A ASP* 2.6 30.4 + - + +
593A TYR* 4.5 16.8 - - + +
594A ARG* 1.3 70.1 - - - +
596A LEU* 1.3 58.9 + - - +
699A ASP* 3.4 3.1 - - - +
700A ILE* 2.6 47.1 + - + -
701A THR* 2.8 26.6 + - + +
736A TYR* 3.2 25.1 + - - -
738A GLY 2.7 30.9 + - - -
739A HIS* 4.3 6.7 + - - +
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Residues in contact with LEU 596 (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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563A LEU* 3.4 4.7 - - - -
564A GLU* 2.7 38.2 + - + +
566A ARG* 3.7 27.8 - - + -
571A LEU* 4.3 4.3 - - + -
580A LEU* 4.0 11.7 - - + -
594A ARG* 3.8 25.4 - - + +
595A ARG* 1.3 83.9 - - - +
597A LEU* 1.3 59.8 + - - +
598A ARG* 3.3 13.9 + - + +
697A TRP* 3.5 59.5 - - + -
698A VAL 3.8 2.2 - - - -
699A ASP* 4.0 5.4 - - - -
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Residues in contact with LEU 597 (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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561A THR* 3.4 33.0 - - + -
562A TYR 3.7 4.7 - - - +
563A LEU* 4.0 11.9 - - + -
595A ARG 4.1 0.8 + - - -
596A LEU* 1.3 68.9 - - - +
598A ARG* 1.3 61.4 - - - +
599A PHE* 3.5 8.2 - - + -
640A LEU* 4.2 17.5 - - + -
697A TRP* 2.9 22.5 - - - +
698A VAL* 2.9 24.5 + - + +
700A ILE* 3.6 25.3 - - + +
710A PHE* 4.5 8.5 - - + -
741A ILE* 4.2 17.3 - - + -
743A MET* 3.9 21.3 - - + -
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Residues in contact with ARG 598 (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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560A THR 4.1 1.1 - - - -
561A THR* 3.2 7.3 - - - +
562A TYR* 2.9 70.7 + - + +
564A GLU* 2.5 31.3 + - + +
566A ARG* 3.4 26.1 - - - +
596A LEU* 4.1 17.8 - - + +
597A LEU* 1.3 75.1 - - - +
599A PHE* 1.3 63.8 + - - +
691A HIS 2.7 28.4 + - - +
692A ASP* 3.2 14.5 + - - -
693A ILE 3.2 19.8 + - - -
694A ASP* 4.5 2.6 + - - -
696A GLN 3.4 11.9 - - - +
697A TRP* 3.3 29.0 - - + -
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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