Contacts of the strand formed by residues 124 - 129 (chain B) in PDB entry 1Q6H
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 VAL 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B ARG* 4.4 19.7 - - + +
110B PHE* 3.7 16.2 - - + -
111B ALA* 4.0 16.8 - - + +
116B VAL* 3.5 25.4 - - + -
117B LYS 3.4 5.4 - - - +
118B THR* 3.9 15.7 - - + +
122B GLY 3.4 11.2 + - - +
123B LEU* 1.3 81.2 - - - +
125B TYR* 1.3 65.4 + - - +
192B LEU* 3.7 0.9 - - - -
193B VAL* 2.8 47.2 + - + +
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 4.9 1.6 - - - -
115B GLY 4.1 0.3 - - - +
116B VAL* 3.5 4.8 - - - -
117B LYS* 2.8 85.4 + - + +
118B THR 4.6 0.6 + - - -
119B SER* 4.2 19.3 - - - -
123B LEU* 4.2 13.7 - - + -
124B VAL* 1.3 79.1 - - - +
126B GLN* 1.3 61.3 + - - +
127B VAL* 4.1 17.9 - - + -
183B ASN* 3.5 37.0 + - + -
190B ILE* 3.9 11.4 - - + -
191B LYS 3.3 10.3 - - - +
192B LEU* 3.9 17.0 - - + -
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Residues in contact with GLN 126 (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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110B PHE* 3.5 21.9 - - + -
113B GLU* 5.9 0.8 + - - +
114B LYS 3.9 17.4 + - - -
115B GLY* 3.8 15.3 - - - +
116B VAL* 4.0 15.7 - - + +
125B TYR* 1.3 76.1 - - - +
127B VAL* 1.3 73.9 + - - +
128B VAL* 3.2 12.2 + - + +
190B ILE* 3.9 2.7 - - - -
191B LYS* 2.9 49.3 + - + +
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Residues in contact with VAL 127 (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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115B GLY 4.3 5.7 + - - +
117B LYS* 6.1 1.3 - - + -
125B TYR* 4.1 25.0 + - + -
126B GLN* 1.3 76.8 - - - +
128B VAL* 1.3 62.6 + - - +
129B GLU 3.9 15.0 - - - +
130B ALA* 3.9 9.4 - - + +
183B ASN* 3.9 18.6 - - + +
184B ILE* 3.8 21.5 - - + -
189B LYS 4.0 2.9 - - - -
190B ILE* 4.0 4.9 - - + -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLN* 3.2 22.9 + - + +
127B VAL* 1.3 76.3 - - - +
129B GLU* 1.3 74.0 + - + +
189B LYS* 2.8 32.4 + - + +
190B ILE* 4.6 1.1 - - - +
191B LYS* 4.6 10.3 - - + +
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Residues in contact with GLU 129 (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 VAL* 3.9 2.9 - - - -
128B VAL* 1.3 89.5 - - + +
130B ALA* 1.3 60.9 + - - +
131B GLY 4.6 1.8 - - - +
184B ILE* 3.5 4.7 - - - +
187B GLY 3.9 5.6 - - - +
188B GLY* 3.1 8.0 - - - -
189B LYS* 2.8 78.0 + - + +
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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