Contacts of the strand formed by residues 130 - 141 (chain B) in PDB entry 2P7I
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 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ARG* 3.5 16.7 + - - -
103B TYR 3.8 2.7 - - - +
106B ILE* 3.7 19.1 - - + -
125B ILE* 2.9 25.3 + - + +
126B ASN* 4.3 4.4 + - - +
129B TRP* 1.3 72.2 - - - +
131B ALA* 1.3 66.6 + - - +
134B GLY* 3.6 28.0 - - - +
135B ARG 3.6 17.7 - - - +
136B LEU* 3.9 5.8 - - + +
190B LEU* 3.9 22.4 - - + -
244B GLU* 4.0 4.0 - - - -
245B LYS* 3.7 49.3 + - + +
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Residues in contact with ALA 131 (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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102B ARG* 3.8 16.2 - - + +
103B TYR 2.8 33.8 + - - +
104B ASP* 3.8 17.5 - - - +
129B TRP 3.3 2.6 + - - -
130B LEU* 1.3 81.2 - - - +
132B GLU* 1.3 67.0 + - - +
133B GLY 3.3 0.5 + - - -
134B GLY* 2.9 17.4 + - - +
245B LYS* 4.4 5.2 - - - +
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Residues in contact with GLU 132 (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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41B ARG* 5.0 3.3 + - - -
102B ARG* 5.3 2.3 - - - +
104B ASP* 4.7 4.3 - - - +
130B LEU 3.9 0.2 + - - -
131B ALA* 1.3 79.4 - - - +
133B GLY* 1.3 59.6 + - - +
134B GLY 3.1 2.3 + - - -
245B LYS* 3.7 31.9 + - - +
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Residues in contact with GLY 133 (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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41B ARG* 3.0 38.4 + - - -
104B ASP* 5.8 0.7 - - - -
131B ALA 3.3 0.8 + - - -
132B GLU* 1.3 72.3 + - - +
134B GLY* 1.3 64.6 + - - +
135B ARG* 4.1 4.2 + - - +
244B GLU* 4.9 8.8 - - - +
245B LYS* 5.8 2.4 - - - +
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Residues in contact with GLY 134 (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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41B ARG* 4.7 0.2 - - - -
103B TYR 4.0 6.5 - - - -
104B ASP* 3.1 22.0 - - - -
130B LEU* 3.6 11.7 - - - +
131B ALA 2.9 16.0 + - - +
132B GLU 3.1 2.6 + - - -
133B GLY* 1.3 83.1 - - - +
135B ARG* 1.3 62.2 + - - +
244B GLU* 3.7 17.8 - - - +
245B LYS* 4.3 3.5 + - - +
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Residues in contact with ARG 135 (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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37A THR* 4.5 4.8 + - - +
38A PRO* 3.1 44.8 + - - +
40A PHE 5.9 0.4 + - - -
38B PRO 4.9 0.2 + - - -
39B PHE* 2.7 43.0 + - - +
40B PHE 4.8 1.2 + - - -
41B ARG* 3.5 32.2 - - + +
104B ASP 2.9 9.4 + - - +
105B ASN* 3.3 3.5 - - - -
106B ILE 2.8 30.3 + - - -
130B LEU* 3.6 5.7 - - - +
133B GLY 4.1 2.1 + - - +
134B GLY* 1.3 78.9 - - - +
136B LEU* 1.3 54.3 + - - +
137B PHE* 3.6 17.8 - - + -
242B LEU* 4.1 17.5 - - + -
243B CYS 3.3 4.3 - - - +
244B GLU* 3.9 27.6 + - + -
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Residues in contact with LEU 136 (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* 3.4 35.2 - - + +
108B LEU* 4.1 16.6 - - + -
122B LEU* 4.1 15.9 - - + -
125B ILE* 3.9 27.6 - - + -
130B LEU* 3.9 7.2 - - + +
135B ARG* 1.3 71.4 - - - +
137B PHE* 1.3 64.6 + - - +
138B LEU* 4.1 16.6 - - + -
190B LEU* 3.8 29.2 - - + -
241B LEU 3.5 1.4 - - - +
242B LEU* 3.5 9.5 - - - +
243B CYS* 2.9 43.0 + - + +
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Residues in contact with PHE 137 (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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36B PHE* 3.6 66.4 - + + -
39B PHE* 3.7 21.5 - - + -
40B PHE* 3.7 16.8 - + - -
105B ASN* 3.6 20.9 - - + -
106B ILE 2.7 23.2 + - - +
107B VAL* 3.8 8.9 - - + -
108B LEU 2.9 28.6 + - - +
109B THR* 4.3 3.6 - - - +
135B ARG* 3.6 19.5 - - + -
136B LEU* 1.3 71.8 - - - +
138B LEU* 1.3 59.8 + - - +
139B VAL* 3.8 1.9 + - - -
240B PHE* 3.9 6.7 - + - -
241B LEU 4.1 1.8 - - - -
242B LEU* 3.7 20.4 - - + -
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Residues in contact with LEU 138 (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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108B LEU* 3.6 35.0 - - + +
112B LEU* 4.1 18.2 - - + -
122B LEU* 4.2 18.8 - - + -
136B LEU* 4.1 15.0 - - + -
137B PHE* 1.3 71.7 - - - +
139B VAL* 1.3 62.5 + - - +
140B CYS* 4.6 2.7 - - - -
181B LEU* 3.8 32.8 - - + +
185B ALA* 4.5 12.3 - - + -
239B ILE 3.7 0.9 - - - +
240B PHE* 3.4 3.5 - - - -
241B LEU* 2.9 55.0 + - + +
243B CYS* 4.6 1.1 - - - -
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Residues in contact with VAL 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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32B MSE 4.0 17.9 - - + -
36B PHE* 3.5 38.6 - - + -
108B LEU 3.0 10.3 + - - +
109B THR* 3.6 10.8 - - + -
110B HIS* 2.8 30.8 + - + -
138B LEU* 1.3 81.0 - - - +
140B CYS* 1.3 65.8 + - - +
198B ILE* 4.2 8.3 - - + -
238B SER* 3.6 23.1 - - - -
239B ILE 3.2 10.1 - - - +
240B PHE* 3.7 14.1 - - + -
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Residues in contact with CYS 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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110B HIS* 3.8 6.7 - - - -
112B LEU* 3.9 15.0 - - - -
113B GLU* 3.4 17.5 - - - +
138B LEU* 4.6 3.1 - - - -
139B VAL* 1.3 78.9 - - - +
141B PRO* 1.3 77.5 - - + +
176B TYR* 3.8 32.8 - - + -
181B LEU* 3.9 21.7 - - + +
238B SER* 3.2 2.1 - - - -
239B ILE* 2.9 32.3 + - + +
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Residues in contact with PRO 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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110B HIS* 3.7 20.6 - - + +
113B GLU* 3.2 33.9 - - + +
140B CYS* 1.3 93.4 - - + +
142B ASN* 1.3 61.3 + - - +
143B ALA 3.8 0.2 + - - -
172B HIS* 4.6 14.8 - - + -
175B THR* 4.7 7.2 - - + +
176B TYR* 3.3 18.4 + - - +
237B ALA 3.7 9.0 - - - +
238B SER* 4.0 4.5 - - - +
239B ILE* 4.6 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