Contacts of the strand formed by residues 118 - 123 (chain C) in PDB entry 1I3R
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 ASN 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C VAL* 1.3 78.5 - - - +
119C VAL* 1.3 60.2 + - - +
120C THR* 5.1 3.3 + - - +
164C GLU 3.5 1.6 - - - +
165C VAL* 3.4 3.3 - - - +
166C ASP* 2.8 45.1 + - + +
1J NAG 1.4 69.6 + - - +
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Residues in contact with VAL 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ILE* 3.3 26.5 - - + -
117C VAL* 3.9 13.8 + - + +
118C ASN* 1.3 76.5 - - - +
120C THR* 1.3 70.7 + - - +
121C TRP* 5.1 3.6 - - + +
149C HIS* 3.3 49.0 + - + +
163C CYS* 3.8 26.5 - - - -
164C GLU 3.3 4.3 - - - +
165C VAL* 4.4 3.4 - - + -
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Residues in contact with THR 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ASN* 5.1 2.9 - - - +
119C VAL* 1.3 81.0 + - - +
121C TRP* 1.3 72.5 + - - +
122C LEU* 4.0 17.8 - - + +
127C PRO* 4.8 10.5 - - + -
162C ASP 3.6 1.0 - - - +
163C CYS* 3.6 0.6 - - - -
164C GLU* 2.7 56.6 + - + +
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Residues in contact with TRP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL* 4.3 8.1 - - + -
105C LEU* 3.6 41.5 - - + -
106C ILE 4.0 2.0 - - - -
107C CYS* 3.4 35.7 - - + -
119C VAL* 4.4 2.0 + - + -
120C THR* 1.3 76.2 - - - +
122C LEU* 1.3 70.1 + - - +
127C PRO* 3.5 1.6 - - - +
128C VAL* 3.1 37.1 + - + +
132C VAL* 3.8 23.8 - - + -
149C HIS* 3.5 29.6 - + + +
150C TYR 3.4 18.9 + - - +
151C LEU* 3.6 28.0 - - + -
162C ASP 3.4 15.7 - - - -
163C CYS* 3.8 19.7 - - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C THR* 4.0 12.1 - - + +
121C TRP* 1.3 82.5 - - - +
123C ARG* 1.3 61.0 + - - +
124C ASN 4.1 0.4 - - - -
125C GLY* 4.3 7.9 - - - +
126C ARG* 3.2 11.4 - - - +
127C PRO* 3.3 35.9 - - + -
128C VAL* 4.2 1.8 - - - -
151C LEU* 5.5 0.2 - - - -
161C TYR* 3.2 8.9 - - - +
162C ASP* 2.6 56.0 + - + +
164C GLU* 4.5 13.0 - - + +
175C ARG* 3.8 38.8 - - - +
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Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LEU* 1.3 71.2 - - - +
124C ASN* 1.3 90.0 + - - +
126C ARG* 2.7 25.9 + - - +
128C VAL* 3.3 38.7 - - + +
130C GLU* 5.3 5.7 + - - +
151C LEU* 5.4 1.4 - - - +
152C THR 4.9 10.9 + - - -
153C PHE* 5.8 2.2 - - - +
159C ASP* 4.9 4.5 - - + -
160C PHE 3.7 3.6 - - - +
161C TYR* 3.9 35.7 + - + -
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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