Contacts of the strand formed by residues 114 - 119 (chain F) in PDB entry 3EBL
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 PRO 114 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113F PHE* 1.3 103.7 - - + +
115F VAL* 1.3 60.8 + - - +
116F ILE* 4.0 3.8 - - + -
145F SER* 3.6 39.7 - - - +
146F LYS 4.5 0.2 - - - +
147F GLY* 3.4 4.5 - - - -
148F VAL 3.1 14.9 + - - +
191F ARG 3.5 6.3 - - - +
193F PHE* 3.7 27.8 - - + -
348F LEU* 4.1 14.6 - - + +
352F LEU* 3.5 17.7 - - + -
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F PHE* 3.7 15.9 + - + +
114F PRO* 1.3 74.4 - - - +
116F ILE* 1.3 65.9 + - - +
117F ILE* 3.8 3.4 + - + -
148F VAL* 3.3 9.6 - - + +
150F VAL* 4.2 13.5 - - + -
176F VAL* 3.7 27.1 - - + -
182F MET* 3.6 43.7 - - - +
190F ALA* 4.2 7.9 - - + -
191F ARG 3.0 9.5 + - - +
192F VAL* 3.4 7.7 - - + +
193F PHE 2.9 26.3 + - - +
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Residues in contact with ILE 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F PRO* 4.7 4.3 - - + +
115F VAL* 1.3 75.0 - - - +
117F ILE* 1.3 62.6 + - - +
118F PHE* 3.6 3.5 + - + +
141F PHE* 4.3 23.8 - - + -
145F SER* 3.8 32.3 - - - +
148F VAL 2.8 11.9 + - - +
149F VAL* 3.4 19.2 - - + +
150F VAL 2.8 26.7 + - - -
193F PHE* 3.5 11.2 - - + +
195F SER* 3.1 31.2 - - - +
222F ILE* 5.0 4.9 - - + -
344F ILE* 6.1 0.4 - - + -
348F LEU* 4.1 26.2 - - + -
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Residues in contact with ILE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F VAL* 4.6 4.7 - - + -
116F ILE* 1.3 72.8 - - - +
118F PHE* 1.3 58.7 + - - +
119F PHE* 3.6 30.2 - - + -
150F VAL* 3.4 7.9 - - + +
152F VAL* 3.7 17.3 - - + -
172F ALA* 4.1 5.2 - - + +
173F LEU* 3.7 31.4 - - + +
176F VAL* 3.8 27.8 - - + -
192F VAL* 3.7 26.7 - - + -
193F PHE 2.8 12.1 + - - +
194F LEU* 3.6 8.9 - - + -
195F SER* 2.8 30.1 + - - +
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Residues in contact with PHE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE* 3.6 2.6 + - + -
117F ILE* 1.3 73.4 - - - +
119F PHE* 1.3 66.1 + - - +
120F HIS* 3.6 19.1 - - + -
134F TYR* 3.6 27.4 - + + -
137F LEU* 3.7 19.7 - - + -
138F CYS* 3.5 30.7 - - - -
141F PHE* 4.0 13.7 - + + -
149F VAL* 4.2 11.2 - - + -
150F VAL 2.9 8.6 + - - +
151F SER* 3.5 10.1 + - - -
152F VAL* 3.1 26.7 + - - +
195F SER* 3.3 18.4 - - - +
196F GLY* 3.7 18.8 - - - -
197F ASP* 3.6 23.1 - - + -
224F LEU* 5.0 2.7 - - + -
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Residues in contact with PHE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F ILE* 3.6 28.0 - - + -
118F PHE* 1.3 76.0 - - - +
120F HIS* 1.3 64.8 + - - +
152F VAL* 3.7 32.5 - - + -
154F TYR* 4.1 17.3 - + + -
165F ALA 5.3 0.2 - - - -
169F GLY* 3.4 37.5 - - - -
194F LEU* 4.4 11.2 - - + -
195F SER 2.8 19.1 + - - -
196F GLY* 3.1 20.8 - - - -
197F ASP 3.4 1.6 + - - -
200F GLY* 3.2 28.5 - - - +
203F ILE* 3.8 21.3 - - + -
204F ALA* 4.3 13.2 - - - -
207F VAL* 4.4 3.6 - - + -
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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