Contacts of the strand formed by residues 563 - 568 (chain 3) in PDB entry 5Z58
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 LEU 563 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5563 ILE 3.6 2.7 - - - +
5573 ALA* 3.6 26.5 - - + -
5613 GLY 4.3 1.6 - - - +
5623 GLU* 1.3 73.3 - - - +
5643 VAL* 1.3 67.1 + - - +
5803 ARG* 3.6 7.4 - - - -
5813 LYS* 2.5 39.8 + - + +
5833 MET* 3.6 38.6 - - + -
5873 VAL* 3.9 10.5 - - + -
5903 MET* 3.9 21.5 - - + -
6053 LEU* 6.1 2.7 - - + -
6073 VAL* 5.6 4.3 - - + -
6173 ILE* 5.5 8.3 - - + -
6193 LEU* 5.8 9.9 - - + -
6253 LEU* 6.1 1.8 - - + -
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Residues in contact with VAL 564 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5363 TRP* 3.8 22.7 - - + -
5393 PRO* 6.2 0.2 - - + -
5543 VAL 3.6 0.9 - - - +
5553 VAL* 4.0 0.5 - - - +
5563 ILE* 2.9 54.6 + - + +
5583 LEU* 4.1 12.3 - - + -
5623 GLU* 3.9 2.6 + - + +
5633 LEU* 1.3 82.7 - - - +
5653 TYR* 1.3 62.4 + - - +
5663 PHE* 3.7 26.7 - - + -
5763 GLU* 3.1 28.7 - - - +
5803 ARG* 4.3 12.8 - - + -
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Residues in contact with TYR 565 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5533 GLN* 2.3 57.3 + - + +
5543 VAL 3.2 8.7 - - - -
5553 VAL* 3.7 15.0 - - + -
5643 VAL* 1.3 76.2 - - - +
5663 PHE* 1.3 65.1 + - - +
5673 GLU* 3.6 29.8 + - + +
5753 ASN 4.8 1.4 - - - +
5763 GLU* 4.5 12.4 + - - +
5773 TYR* 4.9 6.3 + - + +
5923 LEU* 4.0 13.7 - - + +
6013 ARG* 4.4 4.0 - - - +
6023 SER 4.9 1.2 + - - -
6193 LEU* 3.3 60.1 - - + -
6203 ASP* 4.8 4.7 + - - -
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Residues in contact with PHE 566 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5243 ILE* 3.4 34.3 - - + -
5353 GLU 5.4 1.1 - - - -
5363 TRP* 3.2 42.8 - + + -
5523 ARG 4.2 0.9 - - - +
5533 GLN* 2.9 31.6 - - - +
5543 VAL* 2.8 39.5 + - + +
5643 VAL* 3.7 17.9 - - + -
5653 TYR* 1.3 78.0 - - - +
5673 GLU* 1.3 59.2 + - - +
5743 LEU* 3.5 34.8 - - + -
5753 ASN 4.4 4.0 - - - -
5763 GLU* 3.9 17.5 - - + -
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Residues in contact with GLU 567 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5523 ARG* 3.3 25.8 - - - +
5533 GLN* 4.7 1.1 - - + -
5653 TYR* 3.6 28.1 + - + +
5663 PHE* 1.3 74.7 - - - +
5683 MET* 1.3 59.1 + - - +
5693 ASP* 3.9 7.6 + - - +
5743 LEU* 5.1 2.0 - - - -
5753 ASN* 3.0 36.4 + - - +
5773 TYR* 5.7 5.1 - - - +
6013 ARG* 2.3 44.5 + - - -
6193 LEU 5.1 3.3 - - - +
6203 ASP* 6.4 0.4 - - - -
6213 PRO* 5.1 6.9 - - - +
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Residues in contact with MET 568 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5113 LEU* 3.6 34.1 - - + -
5123 GLY* 4.8 10.5 - - - -
5153 ALA* 5.4 3.1 - - + -
5263 HIS* 5.0 0.7 - - - -
5283 ARG* 5.4 0.9 - - - -
5513 GLN 4.5 7.9 - - - +
5523 ARG* 2.6 58.8 + - + +
5673 GLU* 1.3 72.3 - - - +
5693 ASP* 1.3 70.0 + - - +
5723 GLY* 3.2 39.0 - - - +
5733 GLN 4.4 2.7 - - - +
5743 LEU* 4.4 15.9 - - + +
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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