Contacts of the strand formed by residues 114 - 121 (chain B) in PDB entry 2PNT
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
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Residue Dist Surf HB Arom Phob DC
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104B LEU* 3.9 11.7 - - + -
112B PHE* 3.5 30.7 - + + -
113B GLY* 1.3 79.1 - - - +
115B GLU* 1.3 79.0 + - - +
116B ILE* 3.8 27.6 - - + -
135B VAL* 4.4 3.1 - - + -
137B ARG 3.2 14.6 - - - +
138B VAL* 4.0 11.9 - - + -
144B ALA* 3.7 11.0 - - + -
149B LEU* 3.7 18.2 - - + -
155B ILE* 4.2 9.6 - - + -
175B ILE* 4.2 17.7 - - + -
182B LEU* 3.8 19.7 - - + -
184B LEU* 4.8 4.0 - - + -
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Residues in contact with GLU 115 (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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114B PHE* 1.3 83.4 - - - +
116B ILE* 1.3 69.8 + - - +
135B VAL* 3.6 4.5 - - - +
136B CYS* 3.0 37.4 + - - -
137B ARG* 2.9 45.6 + - + +
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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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114B PHE* 3.8 24.9 - - + -
115B GLU* 1.3 81.5 + - - +
117B GLN* 1.3 58.3 + - - +
118B THR* 5.0 0.7 - - + -
133B THR* 3.7 17.0 - - + -
134B PHE 3.2 14.8 - - - +
135B VAL* 4.4 1.1 - - - -
136B CYS* 3.7 7.2 - - - -
155B ILE* 4.0 10.1 - - + -
168B HIS* 2.8 36.9 + - + +
171B ILE* 3.6 35.9 - - + -
172B VAL* 4.1 19.5 - - + +
175B ILE* 4.1 8.1 - - + -
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Residues in contact with GLN 117 (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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116B ILE* 1.3 74.7 - - - +
118B THR* 1.3 88.6 + - - +
119B TYR* 3.5 36.1 - - + +
133B THR* 3.6 1.7 - - - +
134B PHE* 2.9 46.6 + - + +
136B CYS* 3.9 10.7 - - + -
168B HIS* 3.3 33.1 + - - +
169B ARG* 5.7 3.1 + - - +
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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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116B ILE* 5.0 0.7 - - + -
117B GLN* 1.3 90.2 + - - +
119B TYR* 1.3 71.7 + - - +
131B MET* 3.4 26.7 - - - +
132B VAL 3.0 11.2 - - - -
133B THR* 3.4 24.0 - - + +
166B ILE 4.6 1.8 - - - +
167B ARG* 4.4 2.8 - - - -
168B HIS* 3.4 47.8 + - + +
171B ILE* 4.6 1.8 - - + -
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Residues in contact with TYR 119 (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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117B GLN* 3.5 26.5 + - + +
118B THR* 1.3 79.2 - - - +
120B GLY* 1.3 67.7 + - - +
121B LEU 3.5 0.2 + - - -
131B MET* 3.7 7.6 - - - -
132B VAL* 2.8 37.5 + - + +
134B PHE* 3.3 40.3 - + + -
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Residues in contact with GLY 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 TYR* 1.3 77.7 - - - +
121B LEU* 1.3 62.7 + - - +
122B HIS* 3.9 13.3 + - - -
129B VAL* 3.5 22.9 - - - -
130B GLU 3.5 4.7 - - - -
131B MET* 3.6 12.7 - - - +
132B VAL* 5.4 0.2 - - - -
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Residues in contact with LEU 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 TYR 3.5 0.6 + - - -
120B GLY* 1.3 73.0 - - - +
122B HIS* 1.3 69.5 + - - +
123B HIS* 3.9 5.0 + - - -
126B GLU* 4.0 1.6 - - - +
129B VAL* 3.9 1.5 - - - +
130B GLU* 2.8 36.4 + - + +
132B VAL* 4.1 34.5 - - + -
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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
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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