Contacts of the strand formed by residues 198 - 203 (chain A) in PDB entry 3Q72
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 ILE 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A TYR* 3.3 16.8 - - + +
167A ILE* 3.7 27.1 - - + -
184A ARG* 3.4 49.4 - - - +
187A LEU* 3.9 25.6 - - + -
196A VAL* 3.6 14.1 + - + +
197A PRO* 1.3 79.2 - - - +
199A ILE* 1.3 67.0 + - - +
200A LEU* 5.7 0.2 - - - -
226A ASP 4.8 3.0 + - - +
227A CYS* 3.5 11.9 - - - -
228A LYS* 3.0 23.7 + - - +
250A GLN* 5.2 2.0 - - - +
254A ARG* 4.9 3.8 - - - +
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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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164A ALA* 4.7 1.8 - - + -
165A TYR 2.9 14.7 + - - +
166A VAL* 3.5 10.2 - - + +
167A ILE* 2.8 32.9 + - - +
197A PRO* 4.5 6.3 - - + -
198A ILE* 1.3 85.7 - - - +
200A LEU* 1.3 61.6 + - - +
201A VAL* 3.7 9.1 + - + -
228A LYS* 3.5 28.5 - - + +
230A ILE* 4.4 6.1 - - + -
243A LEU* 3.5 27.1 - - + +
246A GLY 5.1 0.4 - - - -
247A VAL* 3.5 42.8 - - + +
250A GLN* 4.5 11.7 - - + -
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Residues in contact with LEU 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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167A ILE* 3.6 21.1 - - + +
169A TYR* 3.8 28.7 - - + -
177A PHE* 4.5 5.2 - - + -
180A ALA* 3.9 21.1 - - + +
181A SER* 5.8 1.1 - - - +
184A ARG* 6.3 1.1 - - + -
198A ILE* 4.1 1.2 + - - -
199A ILE* 1.3 71.9 - - - +
201A VAL* 1.3 59.8 + - - +
218A GLY 3.8 22.0 - - - +
221A CYS* 4.5 12.3 - - + -
222A ALA* 4.4 13.2 - - + +
227A CYS* 4.0 19.4 - - + +
228A LYS 2.7 16.1 + - - +
229A PHE* 3.4 7.6 - - + -
230A ILE 3.0 26.2 + - - +
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Residues in contact with VAL 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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107A LEU* 4.5 11.7 - - + -
166A VAL* 3.8 13.2 - - + -
167A ILE 2.9 13.0 + - - +
168A VAL* 3.4 9.4 - - + -
169A TYR* 2.8 34.9 + - - +
199A ILE* 3.7 7.6 - - + -
200A LEU* 1.3 75.7 - - - +
202A GLY* 1.3 63.0 + - - +
203A ASN 4.1 1.3 - - - +
230A ILE* 3.2 12.1 - - + +
232A THR* 3.4 33.9 - - + +
243A LEU* 3.3 34.3 - - + -
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Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 3.4 35.5 + - - -
171A VAL* 3.7 7.9 - - - +
200A LEU 4.1 0.6 + - - -
201A VAL* 1.3 70.3 - - - +
203A ASN* 1.3 62.6 + - - -
205A SER 4.7 0.3 + - - -
229A PHE* 4.5 0.4 - - - -
230A ILE 2.9 11.1 + - - -
231A GLU* 3.2 14.0 - - - +
232A THR 3.0 22.6 + - - +
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Residues in contact with ASN 203 (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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102A VAL 2.9 24.7 + - - +
103A GLY* 3.6 5.3 - - - -
107A LEU* 3.9 8.7 - - + +
168A VAL* 4.0 11.9 - - + -
169A TYR 2.9 11.6 + - - +
170A SER* 3.7 0.3 - - - -
171A VAL* 3.0 22.0 + - - +
201A VAL* 3.6 1.2 + - + -
202A GLY* 1.3 74.1 - - - +
204A LYS* 1.3 81.2 + - - +
205A SER 3.3 0.2 - - - -
232A THR* 2.8 27.2 + - - +
234A ALA* 3.0 24.7 + - - +
256A GNP 2.9 30.7 + - - -
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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