Contacts of the strand formed by residues 133 - 142 (chain C) in PDB entry 4YCV
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 LEU 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C THR* 3.6 17.9 - - + +
110C ILE* 4.2 18.6 - - + -
115C PHE* 3.7 33.0 - - + -
119C TYR* 4.1 17.0 - - + +
131C THR* 4.3 14.4 - - + -
132C ILE* 1.3 86.8 - - - +
134C ASN* 1.3 63.3 + - - +
135C ILE* 5.2 1.1 - - + +
192C ILE 3.1 3.5 - - - +
193C VAL* 3.4 2.6 - - - -
194C GLY 2.8 36.1 + - - +
196C PRO* 4.0 14.8 - - + -
206C ILE* 5.0 7.1 - - + +
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Residues in contact with ASN 134 (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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106C PHE* 3.7 11.8 - - + -
107C GLU* 3.1 28.9 + - - +
108C ARG 3.7 0.7 - - - -
109C THR* 2.8 59.8 + - + +
110C ILE 3.4 4.2 + - - -
132C ILE* 5.6 2.8 + - - +
133C LEU* 1.3 76.2 - - - +
135C ILE* 1.3 59.0 + - - +
192C ILE 3.1 3.8 - - - -
193C VAL* 3.1 32.0 - - - +
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Residues in contact with ILE 135 (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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106C PHE* 4.2 0.6 - - - -
108C ARG* 4.9 0.7 - - - -
110C ILE* 3.6 24.9 - - + +
112C ILE* 3.9 13.5 - - + -
115C PHE* 3.7 29.6 - - + -
133C LEU* 5.2 1.6 - - + +
134C ASN* 1.3 74.6 - - - +
136C THR* 1.3 73.2 + - - +
154C LEU* 5.1 3.2 - - + +
161C ILE* 3.7 25.8 - - + -
191C GLY* 3.2 1.2 - - - -
192C ILE* 2.8 46.0 + - + +
206C ILE* 3.9 34.1 - - + -
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Residues in contact with THR 136 (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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106C PHE* 3.4 37.7 - - + +
108C ARG* 3.4 34.8 + - + +
112C ILE* 3.9 14.4 - - - +
135C ILE* 1.3 75.3 - - - +
137C GLY* 1.3 58.7 + - - +
154C LEU* 3.2 16.0 - - - +
156C GLY* 5.5 0.3 - - - -
189C ILE* 5.7 2.2 - - - -
190C VAL 3.3 13.0 - - - +
191C GLY* 3.7 1.6 - - - -
214C LEU* 3.8 13.9 - - + -
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Residues in contact with GLY 137 (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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136C THR* 1.3 78.4 - - - +
138C ARG* 1.3 60.9 + - - -
154C LEU* 3.4 15.1 - - - +
155C VAL 3.6 6.3 - - - -
156C GLY* 5.2 2.2 - - - -
189C ILE* 3.5 8.8 - - - +
190C VAL* 2.9 38.7 + - - +
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Residues in contact with ARG 138 (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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137C GLY* 1.3 73.2 - - - -
139C ILE* 1.3 65.0 + - - +
140C MET* 3.3 16.8 + - + +
154C LEU* 3.5 0.7 - - - -
155C VAL* 2.9 38.3 + - + +
187C GLY* 2.8 54.9 + - - +
188C ASP 3.4 4.9 - - - +
189C ILE* 3.3 34.7 - - + +
216C ALA 6.3 0.2 - - - -
217C CYS* 4.6 8.5 - - - +
221C LEU* 4.7 1.2 - - - +
242C LEU* 3.6 41.7 - - + +
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Residues in contact with ILE 139 (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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138C ARG* 1.3 72.1 - - - +
140C MET* 1.3 55.3 + - - +
141C ARG 3.4 25.4 - - - +
142C VAL* 4.7 3.1 - - + +
152C PHE* 3.9 33.9 - - + -
153C ASP 3.4 6.5 - - - +
154C LEU* 4.1 15.9 - - + -
163C VAL* 4.4 3.8 - - + -
184C ILE* 4.0 16.6 - - + -
185C ARG 3.8 15.9 - - - +
186C ARG* 3.4 2.0 - - - -
187C GLY* 2.5 33.5 + - - -
188C ASP 2.9 20.8 + - - +
190C VAL* 4.0 22.9 - - + -
192C ILE* 5.7 0.4 - - + -
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Residues in contact with MET 140 (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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138C ARG* 3.3 20.6 + - + +
139C ILE* 1.3 75.9 - - - +
141C ARG* 1.3 61.0 + - + +
153C ASP* 2.9 7.3 + - + +
155C VAL* 3.6 35.4 - - + -
186C ARG* 2.9 58.6 + - - +
221C LEU* 3.6 28.3 - - + -
242C LEU* 4.8 20.0 - - + +
243C ILE* 4.6 18.8 - - + -
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Residues in contact with ARG 141 (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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139C ILE* 3.4 9.0 - - - +
140C MET* 1.3 81.8 - - - +
142C VAL* 1.3 66.2 + - - +
143C SER* 2.2 33.2 + - - -
151C PHE* 4.1 16.9 - - - +
152C PHE* 3.3 10.5 + - - -
153C ASP* 2.6 83.2 + - + +
162C GLN* 4.6 6.3 - - - +
186C ARG* 4.9 2.5 - - - +
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Residues in contact with VAL 142 (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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139C ILE* 4.7 4.3 - - + -
141C ARG* 1.3 80.4 + - - +
143C SER* 1.3 71.2 + - - +
152C PHE* 3.3 30.7 - - + -
184C ILE 4.7 8.5 - - - +
185C ARG* 5.1 2.2 - - - -
186C ARG* 4.5 27.3 - - + +
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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