Contacts of the strand formed by residues 132 - 140 (chain B) in PDB entry 1FRP
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 ILE 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A SER* 4.1 20.2 - - - +
48B VAL* 4.1 22.4 - - + -
73B LEU* 4.7 6.1 - - + -
120B LEU* 3.6 35.0 - - + -
121B ASP 3.2 12.8 - - - +
122B GLY* 3.3 28.7 - - - +
125B ASN* 4.2 3.8 - - + -
126B ILE* 4.1 19.1 - - + +
130B VAL 3.9 6.3 - - - +
131B SER* 1.3 74.2 - - - +
133B GLY* 1.3 59.3 + - - +
166B LEU* 3.7 8.7 - - - +
167B TYR* 3.0 26.5 + - + +
247B SER* 4.2 0.9 - - - +
249B VAL* 4.9 2.5 - - - -
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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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120B LEU* 3.5 5.6 - - - +
121B ASP* 2.8 30.9 + - - +
132B ILE* 1.3 77.6 - - - +
134B THR* 1.3 62.7 + - - -
165B ALA 3.0 14.4 - - - -
167B TYR* 3.9 10.0 - - - -
249B VAL* 4.0 16.5 - - - +
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Residues in contact with THR 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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37B LEU* 6.5 0.4 - - + -
41B VAL* 5.0 8.1 - - + -
44B ILE* 4.1 5.2 - - + +
81B VAL* 4.6 16.2 - - + -
117B PHE* 5.3 3.8 - - + -
118B ASP 3.5 9.6 - - - +
119B PRO* 3.1 24.7 + - + +
133B GLY* 1.3 71.5 - - - -
135B ILE* 1.3 68.4 + - - +
136B PHE* 4.7 7.1 - - + -
164B TYR* 3.0 7.1 - - - +
165B ALA* 2.8 35.0 + - - -
167B TYR* 2.7 29.8 + - - +
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Residues in contact with ILE 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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116B CYS 4.6 0.2 - - - -
117B PHE* 3.1 5.9 - - - +
118B ASP* 2.8 39.6 + - + +
121B ASP* 3.8 20.9 - - + +
134B THR* 1.3 73.0 - - - +
136B PHE* 1.3 63.0 + - - +
163B GLY 3.7 8.1 - - - +
164B TYR* 4.1 0.7 - - + -
248B MET* 4.3 5.8 - - - -
249B VAL* 3.5 31.6 - - + -
279B TYR 3.4 24.5 - - - +
280B GLU* 4.3 12.3 - - + -
283B PRO* 3.6 22.4 - - + -
284B MET* 4.2 22.2 - - + -
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Residues in contact with PHE 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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34B LEU* 5.4 1.1 - - + -
37B LEU* 3.6 38.6 - - + -
41B VAL* 5.6 2.7 - - + -
115B VAL* 4.7 9.0 - - + -
116B CYS 3.2 9.0 - - - +
117B PHE* 4.2 9.2 - - + -
134B THR* 4.7 10.5 - - + -
135B ILE* 1.3 79.4 - - - +
137B GLY* 1.3 59.1 + - - +
138B ILE* 4.3 21.3 - - + -
162B ALA* 3.4 8.7 - - - -
163B GLY* 3.0 68.8 + - - +
164B TYR* 3.6 13.0 - - - -
165B ALA 4.8 0.4 - - - -
173B LEU* 4.8 10.5 - - + -
174B VAL 4.4 2.7 - - - -
175B LEU* 4.1 22.0 - - + -
283B PRO* 3.5 12.2 - - - +
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Residues in contact with GLY 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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114B VAL 3.9 0.3 - - - +
115B VAL* 3.5 3.1 - - - +
116B CYS* 2.8 40.1 + - - +
136B PHE* 1.3 74.6 - - - +
138B ILE* 1.3 63.3 + - - +
139B TYR* 4.3 0.4 + - - -
159B LEU* 3.8 15.5 - - - -
161B ALA 3.6 8.5 - - - -
162B ALA* 4.1 4.0 - - - -
278B LEU 5.3 0.2 - - - -
283B PRO* 4.0 9.2 - - - +
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Residues in contact with ILE 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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30B MET* 4.3 8.7 - - + -
33B LEU* 3.8 19.1 - - + -
34B LEU* 4.0 20.9 - - + -
37B LEU* 5.6 3.6 - - + -
113B TYR* 3.8 27.8 - - + -
114B VAL 3.4 6.1 - - - +
115B VAL* 4.1 18.6 - - + -
136B PHE* 4.3 16.6 - - + -
137B GLY* 1.3 76.7 - - - +
139B TYR* 1.3 58.8 + - - +
159B LEU* 3.5 5.4 - - - +
160B VAL* 2.8 33.2 + - + -
161B ALA* 2.8 36.9 + - + +
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Residues in contact with TYR 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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113B TYR* 3.4 10.7 - - - -
114B VAL* 2.8 45.6 + - + +
116B CYS* 4.0 25.4 - - + -
137B GLY 5.3 0.2 - - - -
138B ILE* 1.3 74.8 - - - +
140B ARG* 1.3 59.8 + - - +
152B ALA 3.6 22.0 - - - -
154B GLN* 2.9 48.1 + - + +
155B PRO 3.5 18.6 - - - -
156B GLY* 3.5 13.5 + - - -
158B ASN 3.4 17.9 - - - -
159B LEU* 3.6 28.1 - - + +
160B VAL* 4.4 1.1 - - - -
278B LEU* 4.0 7.6 + - + +
282B ASN* 3.7 10.6 + - - +
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Residues in contact with ARG 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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112B LYS* 3.8 30.6 - - + +
113B TYR* 4.0 8.1 - - + -
114B VAL* 4.7 0.2 - - - -
139B TYR* 1.3 74.7 - - - +
141B LYS* 1.3 72.7 + - - +
142B ASN* 3.1 6.6 + - + +
154B GLN* 3.3 18.4 + - - +
158B ASN 4.8 2.6 + - - +
160B VAL* 4.0 26.8 - - + +
338B AMP 2.9 50.4 + - - -
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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