Contacts of the strand formed by residues 165 - 171 (chain B) in PDB entry 3QI5
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 TYR 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ILE* 3.2 5.6 - - - -
161B ILE* 2.6 47.3 + - + +
162B TYR* 4.6 2.2 - - + -
164B MET* 1.3 115.1 - - + +
166B PHE* 1.3 62.3 + - - +
200B LEU* 3.7 12.4 - - + +
219B SER* 3.3 27.1 - - - +
223B GLN* 3.7 26.2 - - + -
8E T 3.3 33.4 - - - -
9E T 3.5 43.8 + - - -
10E G 4.5 7.3 + - - -
18F A 5.3 2.0 - + - -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B VAL* 4.1 9.9 - - + -
159B TYR 3.3 8.3 - - - +
160B ILE* 3.5 36.3 - - + -
164B MET 4.7 10.3 - - - -
165B TYR* 1.3 76.5 - - - +
167B CYS* 1.3 62.7 + - - +
218B PRO 3.6 2.1 - - - +
219B SER* 2.9 33.0 + - - +
222B CYS* 3.8 21.6 - - + +
223B GLN* 6.0 5.2 - - + -
227B ILE 3.7 13.7 - - - +
228B ASN* 3.6 19.7 - - + -
229B LYS* 3.5 27.4 - - + -
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Residues in contact with CYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B TYR 3.3 3.8 - - - +
158B VAL* 3.3 24.0 - - - -
159B TYR* 3.0 35.4 + - + +
161B ILE* 3.8 22.9 - - - -
166B PHE* 1.3 79.0 - - - +
168B MET* 1.3 60.2 + - - +
169B ASN* 3.8 1.4 - - - +
180B LEU* 3.9 13.0 - - + -
218B PRO* 4.5 9.6 - - - -
219B SER* 4.2 0.9 - - - -
222B CYS* 4.3 1.3 - - - -
7E EDC 4.0 24.5 - - - -
8E T 4.0 10.3 - - - -
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 4.1 34.5 - - + -
156B LEU* 3.8 26.7 - - + -
157B TYR 3.9 1.6 - - - -
158B VAL* 4.3 16.8 - - + -
167B CYS* 1.3 70.8 - - - +
169B ASN* 1.3 66.7 + - - +
170B ILE* 4.5 6.5 - - + -
179B VAL 4.0 0.2 - - - +
180B LEU* 3.5 6.4 - - - +
181B LEU* 3.2 45.4 + - + +
218B PRO 4.7 1.4 + - - -
221B LEU* 4.6 9.9 - - + -
222B CYS* 3.7 19.0 - - - -
227B ILE* 4.3 23.3 - - + -
236B LEU* 4.6 3.1 - - + -
242B VAL* 4.6 11.7 - - + -
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B TYR* 4.4 0.8 - - - -
156B LEU* 3.4 8.7 - - - +
157B TYR* 2.8 49.5 + - + +
159B TYR* 3.6 22.5 - - - -
167B CYS 3.8 2.1 - - - +
168B MET* 1.3 78.2 - - - +
170B ILE* 1.3 65.6 + - - +
178B CYS* 3.5 17.7 - - + -
179B VAL 3.1 4.5 - - - +
180B LEU* 3.3 34.2 - - - +
7E EDC 3.2 29.8 + - - +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PHE* 3.9 19.3 - - + -
98B LEU* 4.7 1.2 - - + +
102B PHE* 4.0 18.6 - - + -
154B GLY* 3.9 23.1 - - - +
155B THR 3.5 2.5 - - - -
156B LEU* 3.7 18.4 - - + -
168B MET* 4.3 5.8 - - + +
169B ASN* 1.3 81.9 - - - +
171B SER* 1.3 75.2 + - - +
172B SER* 3.5 0.3 + - - -
178B CYS* 3.9 2.5 - - - -
179B VAL* 2.8 45.1 + - - +
181B LEU* 3.7 36.6 - - + -
236B LEU* 3.8 10.8 - - + -
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.2 3.8 - - - +
148B GLY 3.4 23.3 + - - -
149B MET* 3.9 4.8 + - - -
151B MET 2.7 24.8 + - - -
152B LYS 3.7 9.7 + - - -
153B PRO* 3.4 0.7 - - - +
154B GLY 2.9 22.6 + - - -
155B THR 2.8 17.2 + - - -
157B TYR* 5.3 1.4 - - - +
169B ASN 4.2 0.2 - - - -
170B ILE* 1.3 77.4 - - - +
172B SER* 1.3 68.9 + - - +
177B ALA 3.7 10.0 + - - -
178B CYS* 4.0 4.6 - - - +
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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