Contacts of the strand formed by residues 197 - 202 (chain A) in PDB entry 1XGG
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 PHE 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ARG* 3.5 9.3 + - - +
156A VAL* 3.5 37.0 - - + +
158A MET* 3.7 34.1 - - + -
179A TYR* 4.4 6.1 - - - -
183A LEU* 3.8 31.4 - - + -
186A LEU* 4.6 5.8 - - + -
187A LEU* 4.8 5.6 - - + -
192A THR* 3.6 21.8 - - + -
196A GLY* 1.3 78.6 - - - -
198A CYS* 1.3 63.1 + - - +
199A ILE* 4.9 4.9 - - + -
225A MET* 6.0 0.4 - - + -
233A ARG* 2.9 53.0 + - + +
234A PHE* 3.5 8.0 - + + +
235A LYS 3.1 25.5 + - - +
236A ALA 4.0 1.2 + - - +
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Residues in contact with CYS 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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151A ASP* 3.1 28.5 - - - +
155A ARG* 3.4 12.3 - - - +
156A VAL 3.2 5.5 + - - +
157A VAL* 3.3 26.5 - - + +
158A MET* 2.9 26.5 + - - +
197A PHE* 1.3 74.1 - - - +
199A ILE* 1.3 69.5 + - - +
200A ILE* 4.5 3.1 - - - -
236A ALA 3.6 5.6 - - - -
238A HIS* 3.6 31.2 - - - -
279A ILE* 4.8 3.6 - - - -
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Residues in contact with ILE 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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158A MET* 3.4 26.5 - - + +
160A PHE* 5.0 2.0 - - + -
179A TYR* 5.4 0.4 - - + -
197A PHE* 4.9 0.7 - - + -
198A CYS* 1.3 81.2 - - - +
200A ILE* 1.3 62.9 + - - +
201A GLU* 3.3 16.6 - - + +
234A PHE* 3.5 12.8 - - + -
236A ALA 3.2 9.6 + - - +
237A ILE* 3.2 9.6 - - + +
238A HIS* 2.9 23.9 + - - -
295A RET 2.4 110.2 - - + -
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Residues in contact with ILE 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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147A LEU* 4.9 4.0 - - + -
157A VAL* 3.8 15.7 - - + -
158A MET 3.3 6.5 + - - -
159A LEU* 3.4 32.3 - - + +
160A PHE 3.2 23.7 + - - +
198A CYS* 4.5 1.8 - - - -
199A ILE* 1.3 77.4 - - - +
201A GLU* 1.3 64.4 + - - +
202A ASN* 4.1 0.8 + - + -
238A HIS* 3.4 34.3 - - + +
240A ILE* 4.3 24.0 - - + -
275A PHE* 3.4 35.0 - - + -
279A ILE* 5.0 2.0 - - + -
288A PHE* 5.1 6.1 - - + -
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Residues in contact with GLU 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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160A PHE* 3.2 34.4 + - - +
162A ILE* 3.8 6.1 - - - +
199A ILE* 3.3 13.9 + - + +
200A ILE* 1.3 84.4 - - - +
202A ASN* 1.3 61.7 + - - +
203A PHE* 3.8 14.8 + - + -
237A ILE* 5.2 2.0 - - + -
238A HIS 3.3 10.4 + - - +
239A PHE* 3.8 39.5 - - + -
240A ILE* 4.4 7.1 + - - +
295A RET 3.1 46.9 - - + +
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Residues in contact with ASN 202 (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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160A PHE 3.4 11.9 + - - +
161A ASN* 3.6 27.8 - - + +
162A ILE* 4.1 10.0 + - - +
163A GLU* 3.8 14.0 + - - +
200A ILE* 4.1 1.2 + - + -
201A GLU* 1.3 72.5 - - - +
203A PHE* 1.3 70.1 + - - +
204A LYS* 3.2 15.7 + - - +
206A PHE* 3.4 17.5 - - - -
240A ILE* 4.5 4.1 - - + +
241A HIS* 2.9 33.7 + - - +
288A PHE* 5.1 18.4 - - + -
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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