Contacts of the strand formed by residues 119 - 126 (chain B) in PDB entry 6Q2N
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 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B GLY 3.5 22.2 - - - +
118B CYS* 1.3 78.2 - - - +
120B LEU* 1.3 67.9 + - - +
121B THR* 4.0 3.3 + - - +
145B CYS* 3.1 5.9 - - - -
146B SER* 2.9 48.0 + - - +
208B CYS* 3.8 6.7 - - - -
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Residues in contact with LEU 120 (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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119B VAL* 1.3 76.7 - - - +
121B THR* 1.3 76.6 + - - +
122B ALA* 5.2 0.9 - - + +
143B ARG* 3.8 37.2 - - + +
144B TYR 3.4 10.8 - - - +
205B ALA 4.3 3.8 - - - +
206B LYS* 3.4 28.7 - - - +
207B ARG* 5.8 0.2 - - - -
208B CYS* 3.8 10.3 - - - -
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Residues in contact with THR 121 (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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119B VAL* 4.3 4.5 + - - +
120B LEU* 1.3 81.3 + - - +
122B ALA* 1.3 71.4 + - - +
123B ILE* 6.2 0.2 - - + -
143B ARG* 3.3 1.7 - - - -
144B TYR* 2.9 77.2 + - + +
146B SER* 3.7 15.1 + - - -
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Residues in contact with ALA 122 (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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120B LEU* 5.1 1.4 - - + +
121B THR* 1.3 85.5 - - - +
123B ILE* 1.3 65.0 + - - +
141B ILE* 5.0 7.0 - - + -
142B PHE 3.5 4.9 - - - -
143B ARG* 3.7 23.1 - - + +
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Residues in contact with ILE 123 (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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163A LEU* 6.5 1.3 - - + -
122B ALA* 1.3 77.4 - - - +
124B HIS* 1.3 76.7 + - - +
125B LEU* 4.2 16.2 - - + -
141B ILE* 3.4 11.5 - - - +
142B PHE* 2.8 65.7 + - + +
144B TYR* 4.4 19.7 - - + +
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Residues in contact with HIS 124 (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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123B ILE* 1.3 80.7 - - - +
125B LEU* 1.3 89.8 + - - +
126B ASN* 5.7 0.2 - - - -
139B GLU* 2.4 36.9 + - - -
140B LEU 3.4 11.4 - - - -
141B ILE* 3.7 17.9 - - + -
159D LYS* 4.5 18.4 - - - -
163D LEU* 4.4 9.6 - - + +
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Residues in contact with LEU 125 (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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159A ILE* 4.7 20.9 - - + -
123B ILE* 4.2 26.3 - - + +
124B HIS* 1.3 91.3 - - - +
126B ASN* 1.3 64.1 - - - +
129B ASP* 4.0 30.1 - - + +
130B LEU* 5.4 6.1 - - + -
139B GLU* 3.3 6.1 - - - +
140B LEU* 2.9 47.4 + - + +
142B PHE* 4.7 13.0 - - + -
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Residues in contact with ASN 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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124B HIS* 5.2 0.5 + - - -
125B LEU* 1.3 78.3 - - - +
127B VAL* 1.3 60.1 + - - +
128B THR* 3.2 26.4 + - + +
129B ASP* 3.0 38.1 + - - +
130B LEU* 3.2 8.3 + - - +
137B LYS 3.8 8.2 - - - +
138B GLU 3.8 4.5 - - - +
139B GLU* 3.2 28.6 - - - +
140B LEU* 3.6 8.1 - - - +
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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