Contacts of the strand formed by residues 192 - 198 (chain A) in PDB entry 2ZB5
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 THR 192 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ASN 4.7 2.7 - - - +
188A CYS* 3.6 37.9 - - + +
189A SER 5.4 0.2 - - - +
190A GLY 3.9 5.6 + - - +
191A PRO* 1.3 78.9 - - - +
193A THR* 1.3 66.8 + - - +
604A VAL* 3.5 24.3 - - + +
605A SER 3.5 5.2 - - - -
607A THR 5.1 1.9 - - - -
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Residues in contact with THR 193 (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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192A THR* 1.3 81.2 + - - +
194A ILE* 1.3 71.3 + - - +
195A ARG* 4.3 13.9 + - + +
604A VAL* 3.4 3.3 - - - -
605A SER* 2.9 53.3 + - - +
607A THR* 4.0 20.2 - - + +
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Residues in contact with ILE 194 (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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193A THR* 1.3 81.2 + - - +
195A ARG* 1.3 61.6 + - - +
549A PHE* 3.6 48.9 - - + -
550A SER 4.8 4.7 - - - +
551A TYR* 3.2 40.0 - - + -
602A MET* 3.9 21.5 - - + -
603A GLY 3.3 16.4 - - - +
604A VAL* 4.0 19.3 - - + -
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Residues in contact with ARG 195 (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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193A THR* 3.8 11.7 + - + +
194A ILE* 1.3 76.5 - - - +
196A GLY* 1.3 60.7 + - - +
197A GLN 3.9 0.3 + - - -
551A TYR* 4.0 2.0 - - - -
576A LYS* 5.3 2.1 + - - -
601A GLY 3.5 2.1 - - - +
602A MET* 3.9 0.2 - - - -
603A GLY* 3.0 31.0 + - - +
605A SER* 3.2 28.8 + - - +
607A THR* 2.9 40.1 + - - +
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Residues in contact with GLY 196 (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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195A ARG* 1.3 74.6 - - - +
197A GLN* 1.3 60.2 + - - -
198A PHE* 3.2 21.7 - - - -
551A TYR* 2.9 31.2 + - - -
600A VAL* 3.8 10.1 - - - -
601A GLY 3.6 5.8 - - - -
602A MET* 4.6 1.1 - - - -
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Residues in contact with GLN 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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195A ARG 3.9 0.6 + - - -
196A GLY* 1.3 71.4 - - - -
198A PHE* 1.3 69.2 + - - +
266A GLY 2.9 28.1 + - - +
267A ALA* 3.8 5.7 - - - +
576A LYS* 2.6 39.1 + - - +
578A TRP* 3.1 27.6 - - + -
600A VAL* 3.3 3.3 - - - -
601A GLY 2.6 38.8 + - - +
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Residues in contact with PHE 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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196A GLY 3.2 16.8 - - - -
197A GLN* 1.3 85.2 + - - +
199A SER* 1.3 65.9 + - - +
551A TYR* 3.8 12.6 - + - -
553A TYR* 3.4 28.9 - + - -
554A PRO* 3.4 30.7 - - + -
555A PHE* 3.4 32.1 - + + -
578A TRP* 4.7 0.7 - - - -
599A MET 3.7 11.9 - - - +
600A VAL* 3.4 24.2 - - + -
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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