Contacts of the strand formed by residues 211 - 215 (chain 3) in PDB entry 1ZBE
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 GLU 211 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453 LEU* 4.2 4.3 - - - -
1013 TYR* 3.1 27.9 - - - +
1023 SER* 2.8 22.6 + - - +
1683 TYR* 2.8 34.8 + - + -
2093 ASP 4.1 6.0 - - - +
2103 PHE* 1.3 80.2 - - - +
2123 LEU* 1.3 71.7 + - - +
2133 ARG* 4.2 9.4 - - - +
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Residues in contact with LEU 212 (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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453 LEU* 4.4 18.0 - - + +
813 LEU* 5.5 0.2 - - + -
913 LEU* 5.4 1.1 - - + +
943 ILE* 3.7 30.5 - - + -
953 ALA* 4.2 12.6 - - + -
983 TYR* 3.7 34.6 - - + -
1003 GLN 3.5 2.5 - - - +
1013 TYR* 3.4 26.7 - - + -
1713 THR* 4.6 7.0 - - + -
2103 PHE* 3.5 28.5 - - + -
2113 GLU* 1.3 82.0 - - - +
2133 ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 213 (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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1191 TYR* 4.9 11.9 + - - -
1201 THR* 4.0 2.2 + - - +
1211 ALA 3.3 21.4 + - - -
983 TYR* 3.6 6.0 - - - +
993 THR 3.3 2.1 + - - -
1003 GLN* 2.5 71.6 + - - +
1683 TYR* 3.5 52.8 + - + -
2113 GLU* 4.2 6.7 - - - +
2123 LEU* 1.3 74.8 - - - +
2143 LEU* 1.3 99.8 - - + +
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Residues in contact with LEU 214 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 PRO* 4.0 12.5 - - + +
911 ASN 4.5 0.7 - - - +
1181 PRO* 6.5 1.1 - - + -
1201 THR* 3.6 25.6 - - - +
983 TYR* 3.2 3.1 - - - -
993 THR* 2.9 38.6 + - + -
1003 GLN* 3.4 38.1 - - - +
2133 ARG* 1.3 98.6 - - + +
2153 PRO* 1.3 76.9 - - + +
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Residues in contact with PRO 215 (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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901 PRO* 4.1 8.3 - - - +
1031 ASN* 4.4 3.2 + - - -
973 TYR 3.2 9.9 - - - +
983 TYR* 3.7 17.4 - - + -
2143 LEU* 1.3 92.0 - - + +
2163 ILE* 1.3 64.3 + - - +
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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