Contacts of the strand formed by residues 197 - 205 (chain A) in PDB entry 3QWR
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PHE* 3.8 24.0 - - + -
82A LEU 3.7 5.8 - - - +
84A LYS* 3.8 26.5 - - + +
93A ASP* 3.7 24.0 - - - +
94A ILE* 3.9 25.1 - - + +
126A ILE* 5.5 1.0 - - - +
192A ALA 3.7 0.5 - - - +
193A VAL* 3.4 6.2 - - - -
194A HIS* 2.9 55.4 + - - +
195A LYS 3.5 0.4 - - - -
196A LEU* 1.4 75.5 - - - +
198A TYR* 1.3 70.0 + - - +
199A GLU* 4.4 6.1 - - + +
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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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2A TRP* 3.5 26.3 - + - -
4A LEU* 3.9 21.5 - - + -
10A VAL* 4.1 10.3 - - + -
81A LEU* 4.2 19.7 - - + -
82A LEU 2.8 20.0 + - - +
83A HIS* 3.3 40.6 - + + -
84A LYS 4.6 1.0 + - - -
191A ASP* 2.6 36.6 + - + -
192A ALA 3.5 7.6 - - - -
193A VAL* 4.0 12.8 - - + -
196A LEU 3.9 1.2 + - - -
197A LYS* 1.3 76.5 - - - +
199A GLU* 1.3 82.5 + - - +
200A ASN* 2.7 32.6 + - + +
1C NAG 3.5 0.2 - - - -
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Residues in contact with GLU 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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83A HIS* 4.2 4.7 - - + -
91A SER* 3.2 37.5 - - - +
93A ASP* 2.6 31.4 + - - +
94A ILE* 2.8 33.5 + - + +
191A ASP 3.8 0.2 - - - -
192A ALA 2.8 32.0 + - - +
197A LYS* 4.4 6.7 - - + +
198A TYR* 1.3 90.9 - - - +
200A ASN* 1.3 63.7 + - - +
201A TYR* 2.6 35.5 + - + -
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Residues in contact with ASN 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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83A HIS* 4.2 7.8 + - - -
90A TRP* 5.9 2.8 - - - +
91A SER 4.9 4.8 + - - +
92A THR* 5.2 2.3 - - - +
189A MET* 6.2 1.8 - - + -
190A VAL 3.4 10.5 - - - +
191A ASP* 4.1 2.9 - - - +
198A TYR* 2.7 21.0 + - + +
199A GLU* 1.3 74.3 - - - +
201A TYR* 1.3 75.4 + - - +
202A THR* 5.1 7.0 - - - +
1C NAG 1.4 62.0 + - + +
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Residues in contact with TYR 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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92A THR* 3.2 36.5 - - + -
94A ILE* 4.8 0.2 - - + -
95A LEU* 3.1 54.8 + - + -
106A PHE* 4.0 19.5 - + + -
107A LEU* 3.7 22.8 - - + +
189A MET* 3.4 4.5 - - - +
190A VAL* 2.7 40.3 + - + +
192A ALA* 4.0 13.7 - - + -
199A GLU* 2.6 41.4 + - + -
200A ASN* 1.3 83.2 - - - +
202A THR* 1.3 62.0 + - - +
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Residues in contact with THR 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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107A LEU* 3.8 6.8 - - - +
187A GLU* 4.8 8.8 + - - +
188A VAL 3.1 14.0 + - - -
189A MET* 4.7 7.5 - - - +
200A ASN* 5.1 7.0 - - - +
201A TYR* 1.3 78.5 - - - +
203A SER* 1.3 68.2 + - - +
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Residues in contact with SER 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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107A LEU* 4.0 29.2 + - - +
109A CYS* 4.5 4.8 - - - -
187A GLU* 3.5 3.5 - - - +
188A VAL* 2.8 39.7 + - - +
202A THR* 1.3 79.7 + - - +
204A SER* 1.3 61.8 + - - +
205A PHE* 3.9 17.0 - - - -
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Residues in contact with SER 204 (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* 3.9 1.0 - - - +
186A ILE 3.3 7.4 + - - -
187A GLU* 2.6 34.7 + - - -
202A THR* 5.8 0.2 - - - -
203A SER* 1.3 77.7 + - - +
205A PHE* 1.3 63.5 + - - +
80D LYS* 3.4 29.3 - - - +
81D TYR* 2.8 29.0 + - - -
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Residues in contact with PHE 205 (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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109A CYS* 3.7 24.9 - - + -
118A PHE* 3.9 15.3 - + - -
185A PRO* 3.8 6.7 - - - -
186A ILE* 2.8 65.5 + - + +
188A VAL* 3.8 19.5 - - + -
203A SER* 3.9 13.9 - - - -
204A SER* 1.3 80.2 + - - +
206A PHE* 1.3 67.2 + - - +
207A ILE* 4.5 12.6 - - + -
209A ASP* 5.6 2.7 - - + -
210A ILE* 3.5 37.5 - - + -
80D LYS 4.9 0.9 - - - +
81D TYR* 3.7 10.3 - - - +
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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