Contacts of the strand formed by residues 117 - 123 (chain F) in PDB entry 3J8B
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 117 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F ARG 4.1 1.3 + - - +
116F VAL* 1.3 79.9 - - - +
118F GLY* 1.3 58.0 + - - +
136F SER* 4.0 2.6 - - - -
137F VAL* 3.0 30.1 + - + +
139F HIS* 4.0 24.6 - - + +
173F TYR 3.4 9.9 - - - +
174F ALA* 4.3 5.6 - - + +
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Residues in contact with GLY 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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117F ILE* 1.3 76.0 - - - +
119F THR* 1.3 60.1 + - - -
135F PHE 3.3 12.3 - - - -
136F SER* 4.2 1.6 - - - -
137F VAL* 3.8 12.6 - - - -
172F TRP* 3.1 11.6 - - - +
173F TYR* 2.9 33.0 + - - +
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Residues in contact with THR 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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118F GLY* 1.3 73.8 - - - -
120F LEU* 1.3 64.1 + - - +
134F CYS* 3.1 8.4 - - - +
135F PHE* 2.8 38.6 + - - +
136F SER 5.1 0.4 - - - -
137F VAL* 5.2 0.8 - - - +
153F ALA* 6.5 1.1 - - - -
169F ILE* 6.2 3.4 - - - -
171F GLY 3.6 9.4 - - - -
172F TRP* 4.2 0.9 - - - +
173F TYR* 4.8 2.7 - - - -
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Residues in contact with LEU 120 (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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119F THR* 1.3 76.9 - - - +
121F LEU* 1.3 61.9 + - - +
131F VAL* 5.2 11.7 - - + -
133F ASN 3.6 9.0 - - - +
134F CYS* 4.2 3.1 - - + +
169F ILE* 3.8 4.3 - - - +
170F LEU* 3.1 25.1 + - + -
171F GLY 3.0 23.1 + - - +
172F TRP* 3.9 9.5 - - - +
173F TYR* 5.2 5.2 - - + +
200F LEU* 5.5 6.5 - - + -
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Residues in contact with LEU 121 (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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120F LEU* 1.3 73.8 - - - +
122F GLY* 1.3 59.0 + - - +
130F GLU 4.7 0.2 - - - -
131F VAL* 3.8 4.5 - - - +
132F THR 2.9 22.0 + - - -
133F ASN* 2.9 28.5 + - + +
134F CYS* 4.4 2.2 - - - +
160F HIS* 6.4 2.0 - - + -
167F GLU* 4.1 22.0 - - + +
168F LEU 3.0 13.7 - - - +
169F ILE* 5.0 0.9 - - - -
170F LEU* 4.5 2.9 - - - +
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Residues in contact with GLY 122 (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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121F LEU* 1.3 77.4 - - - +
123F THR* 1.3 61.3 + - - -
130F GLU 3.2 11.2 - - - -
132F THR* 4.1 10.8 - - - -
166F ASN 3.6 7.9 - - - +
167F GLU* 4.1 5.1 - - - -
168F LEU* 2.9 35.6 + - - +
170F LEU* 4.6 5.6 - - - +
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Residues in contact with THR 123 (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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122F GLY* 1.3 74.0 - - - -
124F VAL* 1.3 60.4 + - - +
125F ASP* 3.5 6.7 - - - -
128F SER 4.0 3.6 - - - +
129F VAL* 3.5 2.1 - - - -
130F GLU* 2.9 42.5 + - - +
166F ASN 5.1 4.9 - - - -
168F LEU* 5.5 1.6 - - - -
170F LEU* 5.1 2.1 - - - +
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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