Contacts of the strand formed by residues 172 - 181 (chain F) in PDB entry 4WFH
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 172 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LYS* 6.6 0.4 - - - -
104F GLU* 3.1 36.2 + - - +
137F ASN 3.0 6.1 + - - -
138F PHE* 2.8 53.0 + - + +
139F TYR* 3.7 28.3 - + - -
141F LYS* 3.8 49.9 - - + +
162F TRP* 5.9 1.8 - - + -
163F THR* 3.9 15.7 - - - +
164F ASP* 4.2 0.9 - - - -
165F GLN* 3.5 43.1 - - + +
171F THR* 1.3 75.2 - - - +
173F SER* 1.3 64.0 + - - +
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Residues in contact with SER 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F LEU 3.2 12.6 - - - -
136F ASN* 3.7 12.6 - - - -
137F ASN* 3.0 16.7 + - - -
138F PHE* 3.6 4.3 - - - -
162F TRP* 3.5 3.5 - - - +
163F THR* 3.0 38.9 + - - +
171F THR* 4.7 0.3 + - - -
172F TYR* 1.3 80.5 + - - +
174F MET* 1.3 63.5 + - - +
167G HIS* 3.7 19.7 + - - -
169G PHE* 3.8 11.0 - - - -
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Residues in contact with MET 174 (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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134F PHE* 3.7 1.9 - - - -
135F LEU* 2.8 51.0 + - + +
138F PHE* 4.0 2.2 - - + -
143F ILE* 4.2 16.4 - - + +
145F VAL* 4.2 15.7 - - + -
160F ASN* 3.3 37.0 - - + +
161F SER 3.1 13.7 - - - +
162F TRP* 3.6 35.7 - - + -
173F SER* 1.3 75.3 - - - +
175F SER* 1.3 82.0 + - - +
176F SER* 3.8 8.3 - - - -
169G PHE* 3.4 9.0 - - - -
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Residues in contact with SER 175 (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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132F VAL* 5.2 0.9 - - - -
133F CYS 3.3 7.6 - - - -
134F PHE* 4.1 13.5 - - - -
159F LEU 4.7 1.7 + - - -
160F ASN* 3.3 1.2 - - - -
161F SER* 2.9 39.5 + - - -
174F MET* 1.3 84.1 - - - +
176F SER* 1.3 59.8 + - - +
177F THR* 4.2 12.1 + - - -
169G PHE* 3.6 24.8 - - - +
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Residues in contact with SER 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F VAL* 3.5 1.2 - - - +
133F CYS* 2.8 38.0 + - - -
135F LEU* 4.8 0.9 - - - +
145F VAL* 4.0 16.5 - - - +
147F TRP* 3.0 31.0 + - - -
158F VAL* 3.4 5.2 - - - +
159F LEU 3.5 0.4 - - - -
160F ASN* 2.5 22.5 + - - -
174F MET* 3.8 10.1 - - - +
175F SER* 1.3 72.6 - - - +
177F THR* 1.3 62.6 + - - +
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Residues in contact with THR 177 (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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130F SER* 4.2 12.6 - - - +
131F VAL 3.4 7.9 - - - +
132F VAL* 4.0 22.1 - - + +
157F GLY 3.4 3.3 - - - +
158F VAL* 3.3 4.8 - - - -
159F LEU* 2.8 46.6 + - + +
175F SER* 4.2 9.9 + - - -
176F SER* 1.3 76.8 + - - +
178F LEU* 1.3 60.7 + - - +
179F THR* 3.6 18.2 + - - +
144G LEU* 5.0 10.7 - - + +
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Residues in contact with LEU 178 (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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129F ALA 3.7 1.4 - - - +
130F SER* 3.3 1.9 - - - -
131F VAL* 2.6 47.6 + - + +
147F TRP* 3.9 42.8 - - + +
149F ILE* 4.5 20.6 - - + -
154F ARG* 4.2 9.6 - - + -
156F ASN 3.5 24.9 - - - +
157F GLY 3.4 5.6 - - - +
158F VAL* 3.7 11.7 - - + +
177F THR* 1.3 71.1 - - - +
179F THR* 1.3 58.6 + - - +
180F LEU* 3.8 30.3 - - + -
191F TYR* 4.7 5.8 - - + -
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Residues in contact with THR 179 (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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129F ALA 3.8 3.1 - - - +
130F SER* 3.6 20.3 + - - +
157F GLY* 2.7 29.0 + - - +
159F LEU* 5.6 2.1 - - - +
177F THR* 3.8 13.2 + - - +
178F LEU* 1.3 73.3 - - - +
180F LEU* 1.3 75.1 + - - +
146G LYS* 3.9 12.0 + - - +
174G GLN* 3.3 31.5 + - - +
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Residues in contact with LEU 180 (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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128F GLY* 3.9 1.9 - - - -
129F ALA* 2.8 36.6 + - + +
131F VAL* 4.8 3.6 - - + -
149F ILE* 5.3 2.7 - - + -
154F ARG* 4.3 20.0 - - + +
156F ASN 4.9 0.7 - - - +
178F LEU* 3.8 32.3 - - + +
179F THR* 1.3 86.1 - - - +
181F THR* 1.3 69.4 + - - +
184F GLU* 3.4 22.4 - - + +
185F TYR* 4.1 16.8 - - + +
191F TYR* 4.0 32.8 - - + +
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Residues in contact with THR 181 (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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127F GLY 3.7 9.9 + - - -
128F GLY* 4.8 0.4 - - - -
129F ALA* 4.3 1.1 - - - -
180F LEU* 1.3 78.0 - - - +
182F LYS* 1.3 69.3 + - - +
183F ASP* 3.1 17.1 + - + +
184F GLU* 3.2 41.4 + - + +
185F TYR* 3.1 18.7 + - - +
187F ARG* 5.7 0.2 - - - +
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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