Contacts of the strand formed by residues 114 - 118 (chain B) in PDB entry 3QVL
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 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B MET* 3.9 17.5 - - + -
107B ALA* 3.6 32.1 - - + +
108B THR* 4.3 11.2 - - + -
113B ARG* 1.3 76.3 - - - +
115B SER* 1.3 62.7 + - - +
116B ILE* 3.7 31.2 - - + -
131B LEU* 3.7 21.3 - - + -
136B PHE* 4.4 4.3 - - + -
139B HIS* 2.9 34.4 + - + -
140B CYS* 3.3 17.3 - - + -
141B ALA 2.8 23.7 + - - -
177B SER* 3.8 3.1 - - - -
179B ALA* 3.3 18.4 - - + +
181B VAL* 3.6 18.8 - - + -
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 1.3 73.7 + - - +
116B ILE* 1.3 59.7 + - - +
117B VAL* 5.5 0.2 - - - -
142B ALA 3.4 10.4 + - - -
144B HIS* 4.6 3.4 - - - -
171B ALA* 4.2 4.2 - - - +
175B ASP* 2.7 32.8 + - - +
177B SER* 2.7 23.7 + - - -
179B ALA 3.0 6.7 + - - -
180B ILE* 3.4 20.6 - - - +
181B VAL* 2.8 29.6 + - - +
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Residues in contact with ILE 116 (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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80B PHE* 4.0 21.8 - - + -
104B MET* 4.0 23.3 - - + -
114B PHE* 3.7 30.7 - - + -
115B SER* 1.3 72.5 - - - +
117B VAL* 1.3 68.3 + - - +
118B THR* 4.0 8.3 - - + +
124B LEU* 5.9 0.7 - - + -
127B ALA* 4.7 7.4 - - + -
131B LEU* 4.1 3.4 - - + -
140B CYS* 3.9 13.7 - - - -
142B ALA 3.0 10.4 + - - +
143B LEU* 3.6 22.2 - - + -
144B HIS* 2.8 35.7 + - - +
181B VAL* 3.4 16.6 - - + +
183B GLY* 4.4 2.0 - - - -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 1.3 76.3 - - - +
118B THR* 1.3 57.7 + - - +
144B HIS* 3.4 15.0 - - + +
146B ILE* 3.9 26.7 - - + -
164B VAL* 4.4 17.7 - - + +
167B ARG* 4.3 25.6 - - + +
168B CYS* 4.1 12.1 - - - +
171B ALA* 4.9 3.6 - - + -
180B ILE* 4.0 21.8 - - + -
181B VAL 3.0 10.3 + - - +
182B LEU* 3.7 1.9 - - + -
183B GLY 2.7 26.7 + - - -
187B MET* 3.6 8.8 - - - +
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Residues in contact with THR 118 (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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1B 5HY 3.5 6.8 + - - +
80B PHE* 4.9 4.8 - - - -
116B ILE* 4.0 7.2 - - + -
117B VAL* 1.3 76.6 - - - +
119B THR* 1.3 65.3 + - - +
120B LEU 3.9 5.6 - - - +
123B THR* 3.6 23.7 + - - +
124B LEU* 3.8 22.2 - - + +
127B ALA* 5.8 3.4 - - + -
144B HIS 2.8 18.7 + - - +
145B ALA* 3.3 2.2 - - + -
146B ILE* 3.0 28.8 + - - +
183B GLY* 2.8 28.9 + - - -
187B MET* 3.8 5.5 - - - +
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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
------------------------------------------------------------
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