Contacts of the strand formed by residues 149 - 155 (chain B) in PDB entry 1PR1
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 ARG 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B HIS* 2.6 52.2 + - - -
98B VAL* 3.7 17.5 - - - +
99B LYS* 4.0 7.9 - - - +
102B ASP* 2.7 38.6 + - + -
103B VAL 3.0 9.7 + - - +
104B VAL* 3.5 12.5 - - + +
105B ILE* 2.7 34.0 + - - +
147B ASP 5.3 2.2 - - - +
148B ALA* 1.3 76.5 - - - +
150B VAL* 1.3 56.1 + - - +
176B LEU* 4.0 16.9 - - + +
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Residues in contact with VAL 150 (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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105B ILE* 3.4 15.3 - - + +
107B MET* 3.7 33.9 - - + +
134B VAL* 4.0 14.8 - - + -
138B VAL* 3.6 31.2 - - + -
148B ALA 4.0 6.9 + - - +
149B ARG* 1.3 77.6 - - - +
151B GLY* 1.3 60.0 + - - +
176B LEU* 3.6 4.3 - - - +
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Residues in contact with GLY 151 (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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105B ILE 3.1 8.0 + - - -
106B GLY* 3.4 5.6 - - - -
107B MET* 2.9 39.8 + - - -
108B GLY 3.3 3.1 + - - -
150B VAL* 1.3 76.2 - - - +
152B ASN* 1.3 60.3 + - - -
176B LEU* 3.2 14.2 - - - +
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Residues in contact with ASN 152 (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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107B MET* 6.0 0.4 - - - -
108B GLY* 3.0 29.2 - - - -
109B ALA* 3.4 2.9 + - - -
110B CYS* 3.7 23.4 - - - -
151B GLY* 1.3 73.7 - - - -
153B LEU* 1.3 61.8 + - - +
173B TYR 5.5 4.2 + - - +
174B GLY 4.8 4.4 + - - +
175B ILE* 3.3 15.2 - - + +
176B LEU* 2.7 39.0 + - - +
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Residues in contact with LEU 153 (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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104B VAL* 3.8 27.8 - - + +
106B GLY* 3.7 26.5 - - - +
108B GLY 3.0 10.4 + - - +
109B ALA* 4.1 3.8 - - + -
110B CYS* 2.6 35.1 + - - +
152B ASN* 1.3 76.3 - - - +
154B PHE* 1.3 55.5 + - - +
155B SER 4.1 0.2 - - - -
175B ILE* 4.4 2.7 - - - -
177B GLY* 3.3 23.6 - - - +
179B GLU* 4.4 19.3 - - + +
182B ALA* 3.8 14.4 - - + -
186B TYR* 4.9 0.4 - - - +
198B THR* 3.2 27.8 - - + +
200B CYS* 4.6 11.9 - - + -
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Residues in contact with PHE 154 (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 CYS* 3.3 20.6 - - + -
111B THR 4.0 14.4 - - - -
112B ASP* 3.8 29.6 - - + -
153B LEU* 1.3 74.6 - - - +
155B SER* 1.3 58.2 + - - +
156B ALA* 3.7 32.5 - - + -
166B MET* 4.2 26.0 - - + -
170B MET* 3.7 45.1 - - + -
175B ILE* 4.0 14.6 - - + +
177B GLY 2.9 8.2 + - - +
178B VAL* 3.6 4.6 - - + -
179B GLU* 2.9 28.8 + - - +
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Residues in contact with SER 155 (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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66B ILE* 4.1 9.1 - - - +
109B ALA* 4.0 1.4 - - - +
110B CYS 2.6 14.7 + - - -
111B THR* 2.9 25.5 + - - -
112B ASP* 3.3 4.0 + - - +
154B PHE* 1.3 72.8 - - - +
156B ALA* 1.3 60.7 + - - +
179B GLU* 2.7 24.2 + - - -
180B MET 4.1 0.2 - - - -
181B GLU 4.1 9.9 - - - -
182B ALA* 3.3 3.1 + - - +
183B ALA* 2.8 37.6 + - - +
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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