Contacts of the strand formed by residues 193 - 200 (chain A) in PDB entry 4OE4
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 TRP 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A PRO* 3.6 38.8 - - + +
186A VAL* 3.5 26.5 - - - -
187A GLU* 3.5 25.8 - - + -
192A THR* 1.3 73.1 - - - +
194A ASN* 1.3 62.4 + - - +
558A THR* 3.9 1.6 - - - +
559A LYS* 3.7 0.7 - - - -
560A GLU* 2.9 47.9 + - + +
562A PHE* 3.4 34.1 - + + -
498B ARG* 6.1 0.2 - - - -
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Residues in contact with ASN 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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185A PRO* 3.0 8.2 - - - +
186A VAL* 2.9 44.9 + - + +
188A SER* 2.8 27.9 + - - -
192A THR* 3.2 20.8 + - - -
193A TRP* 1.3 75.8 - - - +
195A LYS* 1.3 61.4 + - - +
557A ASN* 6.4 1.1 - - + -
558A THR 3.3 6.5 - - - +
559A LYS* 2.7 41.5 + - - +
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Residues in contact with LYS 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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184A GLN 5.4 1.1 - - - -
185A PRO* 4.0 21.3 - - + -
194A ASN* 1.3 76.8 - - - +
196A ALA* 1.3 65.8 + - - +
197A GLU* 3.4 25.7 + - + +
556A ARG 4.2 0.2 - - - +
557A ASN* 3.6 3.2 - - - +
558A THR* 3.0 49.2 + - + +
505B ASP* 3.4 29.2 + - - -
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Residues in contact with ALA 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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183A GLN* 3.9 26.8 - - + +
184A GLN 5.7 1.2 + - - -
195A LYS* 1.3 79.8 - - - +
197A GLU* 1.3 62.1 + - - +
198A TYR* 5.6 1.5 - - + -
555A ILE* 3.8 15.5 - - + -
556A ARG 3.6 4.7 - - - -
557A ASN* 3.3 20.6 - - - +
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Residues in contact with GLU 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 LYS* 3.4 25.7 + - + +
196A ALA* 1.3 76.7 - - - +
198A TYR* 1.3 66.5 + - - +
199A ARG* 5.0 8.2 - - + +
554A SER 3.7 0.5 - - - +
555A ILE* 3.3 6.6 - - - +
556A ARG* 2.8 72.9 + - + +
558A THR* 5.0 0.4 + - - +
509B LYS* 4.8 9.7 - - - +
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Residues in contact with TYR 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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180A LEU* 3.5 55.1 - - + +
181A TYR* 4.1 31.9 + + + -
196A ALA* 5.6 2.5 - - + -
197A GLU* 1.3 76.8 - - - +
199A ARG* 1.3 59.9 + - - +
200A PRO* 4.7 0.9 - - - +
227A MET* 5.5 0.6 - - + +
550A SER* 5.8 3.8 - - - -
553A VAL* 3.4 35.0 - - + -
554A SER 3.5 5.4 - - - -
555A ILE* 4.0 29.8 - - + +
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Residues in contact with ARG 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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197A GLU* 3.7 11.7 + - + +
198A TYR* 1.3 76.1 - - - +
200A PRO* 1.3 82.1 - - + +
227A MET 4.8 0.2 - - - -
553A VAL* 3.1 8.1 - - - -
554A SER* 2.8 65.6 + - - +
555A ILE 3.7 9.3 + - - -
556A ARG* 3.7 16.1 - - - +
509B LYS* 2.4 44.8 + - + -
510B PHE* 3.6 30.9 + - + +
512B ALA 3.1 17.8 + - - -
513B GLY* 4.0 12.3 - - - +
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Residues in contact with PRO 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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113A LYS* 3.8 13.5 - - - -
117A TYR* 3.9 24.2 - - + -
198A TYR 4.7 0.9 - - - +
199A ARG* 1.3 97.4 - - + +
201A LEU* 1.3 66.7 + - - +
202A GLU 3.7 0.2 + - - -
227A MET 3.5 20.3 - - - +
228A GLY 3.4 26.5 - - - +
229A ASN* 3.5 9.2 - - - +
552A PHE 3.8 6.7 - - - +
553A VAL* 4.3 1.3 - - - -
554A SER* 4.7 2.4 + - - -
510B PHE* 3.4 19.7 - - + -
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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