Contacts of the strand formed by residues 103 - 107 (chain B) in PDB entry 3QI6
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 HIS 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.0 6.3 - - - +
101B GLY 5.1 0.2 - - - +
102B ASP* 1.3 79.3 - - - +
104B VAL* 1.3 67.0 + - - +
105B VAL* 3.8 8.1 - - + -
127B VAL* 4.9 0.7 - - - -
128B GLU* 3.2 20.2 - - + +
129B TYR* 3.6 6.7 - - - -
130B THR* 2.8 30.6 + - - -
143B ALA 3.2 26.9 - - - -
145B ARG* 3.4 33.8 + - - +
147B THR* 3.0 26.6 + - - +
148B THR* 2.6 22.2 + - - +
149B ARG 3.2 22.0 + - - -
150B LEU 3.7 3.1 + - - -
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 5.0 0.9 - - + -
98B LEU* 4.3 23.1 - - + -
103B HIS* 1.3 77.4 + - - +
105B VAL* 1.3 77.6 + - - +
106B ILE* 3.7 12.3 - - + -
118B ILE* 4.3 15.0 - - + -
127B VAL* 4.4 3.8 - - + -
128B GLU 3.0 11.3 + - - +
129B TYR* 3.1 37.5 - - + +
130B THR 3.1 4.7 + - - -
150B LEU* 3.2 27.1 - - + +
152B TRP* 4.0 13.0 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B HIS* 3.8 4.0 - - + -
104B VAL* 1.3 75.8 - - - +
106B ILE* 1.3 61.2 + - - +
130B THR 3.4 7.4 - - - +
132B VAL* 3.6 28.3 - - + -
134B LEU* 4.9 1.1 - - + -
140B VAL* 4.6 8.5 - - + -
143B ALA* 3.6 36.3 - - + +
144B ILE* 4.1 9.6 - - + -
148B THR* 3.8 18.8 - - + -
150B LEU 3.0 7.9 + - - +
151B ILE* 4.2 20.6 - - + +
152B TRP 2.8 28.6 + - - +
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Residues in contact with ILE 106 (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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104B VAL* 3.7 24.9 - - + +
105B VAL* 1.3 79.1 - - - +
107B PRO* 1.3 82.0 - - + +
110B ALA* 5.2 2.7 - - + -
114B THR* 6.1 0.7 - - + -
115B PHE* 3.9 22.9 - - + -
118B ILE* 3.9 27.6 - - + -
129B TYR* 3.5 30.3 - - + -
130B THR 2.8 8.7 + - - +
131B PRO* 3.2 13.8 - - + +
132B VAL* 2.9 30.1 + - - +
134B LEU* 4.7 4.7 - - - -
152B TRP* 3.8 7.4 - - + -
359B GLN* 4.0 2.2 - - - +
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Residues in contact with PRO 107 (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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106B ILE* 1.3 97.2 - - + +
108B ASP* 1.3 60.1 + - - +
109B ASP* 3.2 17.3 + - - +
110B ALA* 3.8 26.6 + - + +
132B VAL 3.7 5.2 - - - +
134B LEU* 4.0 17.0 - - + -
152B TRP* 3.2 28.2 - - + +
154B GLU* 4.1 20.4 - - + +
157B THR* 4.7 5.6 - - + -
359B GLN* 3.2 15.9 + - - -
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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