Contacts of the strand formed by residues 141 - 147 (chain C) in PDB entry 3WHD
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 TYR 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C PRO* 4.1 10.3 - - + +
99C LEU 4.1 9.4 - - - -
100C THR* 4.0 12.8 - - + +
134C PHE 4.4 2.3 + - - -
135C LEU* 3.6 33.3 - - + -
136C ASP* 2.8 51.3 + - - +
139C LEU* 3.8 18.1 - - + +
140C SER* 1.3 77.8 - - - +
142C PHE* 1.3 63.3 + - - +
143C LEU* 3.5 2.1 + - - +
184C VAL* 3.1 3.7 - - - -
185C LEU* 2.8 42.2 + - + +
192C TRP* 4.2 2.5 - + - -
204C SER* 3.6 17.9 - - - -
205C ARG 3.7 18.2 - - - +
206C ILE* 3.9 24.2 - - + -
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Residues in contact with PHE 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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103C LYS 3.5 14.1 - - - -
105C TRP* 3.4 46.7 - + + -
108C SER* 3.8 14.4 - - - +
119C LEU* 4.2 9.8 - - + +
140C SER 4.2 0.2 - - - -
141C TYR* 1.3 72.4 - - - +
143C LEU* 1.3 63.3 + - - +
182C CYS* 3.9 13.9 - - + -
183C VAL 3.6 6.7 - - - -
184C VAL* 3.5 13.1 - - + +
197C VAL* 3.7 30.5 - - + -
198C PRO 4.3 0.4 - - - -
199C CYS 4.3 2.7 - - - -
201C PHE* 3.5 18.4 - - + -
203C ALA* 3.7 15.7 - - + -
204C SER 2.8 24.0 + - - +
205C ARG* 4.0 6.9 - - + -
206C ILE 3.5 20.6 + - - +
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Residues in contact with LEU 143 (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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105C TRP* 2.9 24.6 + - - -
119C LEU* 3.6 7.0 - - - +
120C MET* 3.8 18.4 - - + +
122C ILE* 3.7 26.9 - - + -
141C TYR 4.2 8.1 - - - +
142C PHE* 1.3 81.5 - - - +
144C GLY* 1.3 59.5 + - - +
145C LEU 3.2 9.7 + - - +
156C TRP* 4.3 6.7 - - + -
183C VAL* 2.8 28.6 + - + +
185C LEU* 4.3 10.3 - - + +
194C TRP* 3.6 39.9 - - + +
206C ILE* 4.2 18.4 - - + -
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Residues in contact with GLY 144 (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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105C TRP* 3.9 6.2 - - - -
119C LEU* 3.5 25.3 - - - +
120C MET 2.8 20.0 + - - -
121C THR* 5.4 0.2 - - - -
143C LEU* 1.3 70.8 - - - +
145C LEU* 1.3 60.7 + - - +
146C ARG 3.6 0.5 + - - -
155C ARG 3.5 1.6 - - - +
156C TRP* 3.6 8.5 - - - -
157C VAL* 2.9 34.9 + - - +
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Residues in contact with LEU 145 (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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105C TRP* 4.4 2.3 + - - -
143C LEU* 3.2 3.4 - - + -
144C GLY* 1.3 76.3 - - - +
146C ARG* 1.3 60.4 + - - +
154C TRP* 3.6 46.7 - - + -
155C ARG 3.5 25.4 - - - +
156C TRP* 3.5 37.6 - - + +
162C PHE* 4.0 16.4 - - + -
169C TRP* 4.6 3.4 - - + -
182C CYS* 3.6 2.4 - - - +
183C VAL* 3.3 46.4 + - + +
194C TRP* 4.1 15.5 - - + -
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Residues in contact with ARG 146 (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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105C TRP* 3.6 40.9 - - + -
106C ALA* 6.1 1.2 - - - +
145C LEU* 1.3 76.9 - - - +
147C ASP* 1.3 61.4 + - - +
148C GLU* 3.7 38.5 + - + +
153C GLN 3.5 1.6 - - - +
154C TRP* 3.9 3.4 - - - -
155C ARG* 2.8 42.1 + - - +
180C GLU* 2.7 37.1 + - - -
181C ASN 3.4 12.3 - - - +
182C CYS* 3.7 5.8 - - - -
199C CYS* 3.5 19.7 - - - -
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Residues in contact with ASP 147 (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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146C ARG* 1.3 72.3 - - - +
148C GLU* 1.3 62.7 + - - +
149C ASN* 3.9 2.4 + - - +
150C ALA* 3.3 15.8 + - - -
151C LYS* 3.2 13.7 + - - +
152C GLY* 2.7 28.2 + - - -
153C GLN* 3.1 31.1 + - - +
154C TRP* 3.5 28.1 - - + -
181C ASN* 2.8 37.3 + - + +
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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