Contacts of the strand formed by residues 196 - 201 (chain A) in PDB entry 1ZR3
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 LYS 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A THR* 4.6 4.7 - - + -
189A LYS 3.7 4.3 - - - -
190A SER* 4.5 12.3 - - - +
194A GLY 3.7 5.1 + - - +
195A GLN* 1.3 71.9 - - - +
197A LEU* 1.3 55.7 + - - +
198A GLN* 3.4 29.6 - - + +
344A LYS* 2.7 16.1 + - + +
345A THR* 3.2 16.5 - - + +
346A VAL 2.8 31.9 + - - +
249D ASN* 3.1 36.6 + - - +
251D PRO 3.0 18.7 + - - +
252D LEU* 4.5 2.6 - - - +
253D GLU* 2.7 39.5 + - - +
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Residues in contact with LEU 197 (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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188A THR* 3.2 3.6 - - - -
189A LYS* 2.7 44.0 + - + +
191A LEU* 3.9 32.1 - - + -
195A GLN* 4.5 3.8 - - + -
196A LYS* 1.3 77.8 - - - +
198A GLN* 1.3 62.4 + - - +
328A LEU* 3.7 14.8 - - + -
331A ILE* 4.1 9.4 - - + -
346A VAL* 3.2 22.7 - - + -
348A PHE* 3.8 14.1 - - + -
363A MET* 3.5 20.9 - - + +
366A LEU* 3.6 31.4 - - + -
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Residues in contact with GLN 198 (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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185A VAL* 3.6 20.5 - - + +
187A SER 3.1 5.6 - - - +
188A THR* 2.8 29.0 + - + +
196A LYS* 3.4 20.6 - - + +
197A LEU* 1.3 82.3 - - - +
199A VAL* 1.3 60.6 + - - +
200A VAL* 3.9 0.4 + - - -
345A THR* 3.4 12.5 - - + +
346A VAL 2.8 6.7 + - - -
347A TYR* 3.1 39.3 + - + +
348A PHE* 2.8 32.8 + - - +
363A MET* 4.2 0.4 - - - -
248D LYS 4.3 1.0 + - - -
249D ASN* 2.9 22.8 + - - +
250D GLY* 3.9 0.5 - - - -
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Residues in contact with VAL 199 (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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185A VAL* 3.6 2.9 - - - -
186A LEU* 2.7 36.6 + - + +
187A SER* 3.0 16.4 + - - +
198A GLN* 1.3 73.4 - - - +
200A VAL* 1.3 59.8 + - - +
348A PHE* 3.4 14.1 - - + +
350A LEU* 4.1 7.0 - - + -
356A ILE* 3.5 41.7 - - + +
359A TYR* 4.0 20.2 - - + -
360A VAL* 4.2 10.1 - - + +
363A MET* 3.8 27.1 - - + -
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Residues in contact with VAL 200 (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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183A PHE* 3.7 37.7 - - + -
184A THR 3.6 14.6 - - - +
185A VAL* 4.2 8.5 - - + -
186A LEU* 4.4 0.4 - - - -
198A GLN 4.4 0.9 - - - +
199A VAL* 1.3 81.3 - - - +
201A GLN* 1.3 63.2 + - - +
202A ALA* 3.9 15.7 - - + -
207A ILE* 4.1 4.7 - - + -
347A TYR* 3.7 31.6 - - + -
348A PHE 2.9 8.6 + - - +
349A VAL* 3.2 11.1 - - + -
350A LEU 3.0 23.9 + - - -
356A ILE* 3.6 4.8 - - - +
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Residues in contact with GLN 201 (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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184A THR 4.5 1.0 + - - +
186A LEU* 3.7 20.7 - - + +
200A VAL* 1.3 73.2 - - - +
202A ALA* 1.3 65.1 + - - +
350A LEU 3.2 14.8 - - - +
351A PHE* 2.7 25.5 + - - +
353A SER* 3.7 23.4 + - - +
356A ILE* 3.5 22.5 - - + +
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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