Contacts of the strand formed by residues 138 - 145 (chain B) in PDB entry 2P9R
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 LEU 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ASN 4.1 0.2 + - - -
137B GLU* 1.3 71.9 - - - +
139B ILE* 1.3 60.6 + - - +
140B PRO* 3.4 10.9 - - + +
157B SER* 3.6 45.5 - - - +
158B PHE 3.6 10.3 - - - +
159B GLN* 3.4 26.7 + - + +
187B LYS* 4.4 13.2 - - - +
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Residues in contact with ILE 139 (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 VAL* 4.8 6.5 - - + -
125B VAL* 4.7 5.2 - - + -
137B GLU* 3.4 33.2 - - + +
138B LEU* 1.3 71.1 - - - +
140B PRO* 1.3 66.3 - - - +
141B LEU 3.8 17.0 - - - +
157B SER* 2.9 24.1 + - - -
158B PHE* 2.9 55.8 + - + -
160B LEU* 3.7 22.2 - - + -
184B VAL* 3.9 13.5 - - + -
185B GLN 3.8 5.6 - - - +
186B LYS* 4.4 11.9 - - + -
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Residues in contact with PRO 140 (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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138B LEU* 3.4 9.6 - - + +
139B ILE* 1.3 84.0 - - - +
141B LEU* 1.3 62.3 + - + +
156B GLN* 3.2 10.2 + - - +
157B SER* 2.8 26.3 + - - +
185B GLN* 3.0 25.1 - - + +
186B LYS* 3.7 1.8 - - - +
187B LYS* 3.5 34.5 - - + +
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Residues in contact with LEU 141 (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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139B ILE* 3.5 8.9 - - - +
140B PRO* 1.3 85.2 - - + +
142B VAL* 1.3 70.0 + - - +
143B TYR* 3.9 24.5 - - + -
151B ARG* 3.9 13.2 - - - +
154B GLN* 3.2 39.5 - - + +
155B TRP 3.5 8.3 - - - +
156B GLN* 4.0 12.8 - - + +
158B PHE* 4.3 0.7 - - - -
184B VAL* 3.6 0.7 - - - -
185B GLN* 2.9 52.2 + - + +
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Residues in contact with VAL 142 (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 PHE* 3.9 21.5 - - + -
125B VAL* 4.1 3.6 - - + -
141B LEU* 1.3 76.8 - - - +
143B TYR* 1.3 67.8 + - - +
154B GLN* 3.5 0.2 - - - -
155B TRP* 2.9 54.9 + - + -
158B PHE* 3.4 28.7 - - + -
167B PHE* 4.0 9.6 - - + -
182B VAL* 4.0 7.6 - - + -
183B VAL 3.1 13.0 - - - +
184B VAL* 3.8 20.4 - - + -
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Residues in contact with TYR 143 (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 PHE* 5.7 0.2 - - - -
141B LEU* 3.9 25.1 - - + -
142B VAL* 1.3 76.5 - - - +
144B ILE* 1.3 71.3 + - - +
145B GLN* 3.7 20.7 + - + -
151B ARG* 3.4 52.8 + - - +
153B ALA 3.2 17.0 - - - +
154B GLN* 3.8 10.8 - - + +
155B TRP* 4.6 3.1 - - - -
181B LYS 3.4 0.2 - - - +
182B VAL* 3.3 4.9 - - - -
183B VAL* 2.8 77.3 + - + +
185B GLN* 6.1 1.6 - - + -
191B ARG* 4.0 11.1 + - - -
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Residues in contact with ILE 144 (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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121B VAL* 4.7 11.4 - - + -
123B PHE* 3.9 30.5 - - + -
143B TYR* 1.3 77.6 - - - +
145B GLN* 1.3 62.2 + - - +
151B ARG* 3.4 6.4 - - - -
152B ILE* 3.1 49.8 + - + +
153B ALA* 3.1 8.8 + - + +
155B TRP* 4.3 7.2 - - + -
169B PHE* 3.7 36.8 - - + -
180B TYR* 4.2 5.4 - - + -
181B LYS 3.2 6.7 - - - +
182B VAL* 4.4 7.2 - - + -
196B PHE* 3.9 22.4 - - + -
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Residues in contact with GLN 145 (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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143B TYR* 3.7 28.9 + - + -
144B ILE* 1.3 74.0 - - - +
146B ASP* 1.3 61.3 + - - +
149B GLY* 3.5 39.6 - - - +
150B ASN 3.2 6.7 - - - +
151B ARG* 4.8 3.3 - - - +
180B TYR* 3.2 10.0 - - - +
181B LYS* 2.8 63.4 + - + +
183B VAL* 5.1 0.2 - - - +
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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