Contacts of the strand formed by residues 130 - 139 (chain L) in PDB entry 1W72
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 ALA 130 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120L PRO* 3.8 20.0 - - + -
124L GLU* 3.7 4.0 + - - -
125L LEU* 3.9 12.3 - - + -
129L LYS* 1.3 79.3 - - - +
131L THR* 1.3 64.6 + - - +
132L LEU* 5.7 0.2 - - - -
180L SER* 3.5 3.3 - - - -
181L LEU* 2.9 55.7 + - + +
182L THR 4.3 5.8 - - - +
183L PRO 4.4 0.7 - - - -
186L TRP* 4.5 4.0 - - + -
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Residues in contact with THR 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H LEU* 5.9 0.5 - - - +
143H LEU* 4.1 12.5 - - + +
145H LYS* 3.8 14.4 + - + -
119L PRO 4.0 2.4 - - - +
120L PRO* 3.5 20.5 - - - +
124L GLU* 2.6 31.3 + - - +
130L ALA* 1.3 77.9 + - - +
132L LEU* 1.3 74.5 + - - +
133L VAL* 4.1 10.1 + - + +
178L TYR* 4.0 26.9 - - + -
179L LEU 3.3 8.5 - - - +
180L SER* 4.6 8.6 + - - +
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Residues in contact with LEU 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L LEU* 4.3 0.9 - - + -
118L PHE 3.4 7.9 - - - +
119L PRO* 4.0 4.9 - - + -
120L PRO* 3.3 36.8 - - + -
131L THR* 1.3 73.7 - - - +
133L VAL* 1.3 61.8 + - - +
148L TRP* 3.6 28.0 - - + -
178L TYR* 3.3 6.1 - - - -
179L LEU* 2.8 37.6 + - + +
181L LEU* 4.1 12.6 - - + -
186L TRP* 3.7 15.9 - - + -
192L TYR* 3.4 42.6 - - + -
209L VAL* 4.2 6.5 - - + -
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Residues in contact with VAL 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 4.5 14.4 - - + -
143H LEU* 4.1 14.8 - - + -
188H SER* 3.3 22.9 - - - +
116L THR 3.3 2.4 - - - +
117L LEU* 3.3 4.3 - - - -
118L PHE* 2.8 46.1 + - + +
131L THR* 4.1 14.1 - - + +
132L LEU* 1.3 77.0 - - - +
134L CYS* 1.3 63.2 + - - +
135L LEU* 3.8 23.1 - - + -
177L SER 3.8 2.2 - - - -
178L TYR* 3.7 26.9 - - + -
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Residues in contact with CYS 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L VAL* 3.6 22.7 - - - -
116L THR 3.4 2.9 - - - -
117L LEU* 4.0 2.5 - - + -
132L LEU 4.1 0.2 + - - -
133L VAL* 1.3 74.4 - - - +
135L LEU* 1.3 60.0 + - - +
136L ILE* 4.2 6.7 + - - +
148L TRP* 3.6 13.2 - - + -
176L SER* 3.4 5.5 - - - -
177L SER* 2.8 45.3 + - - +
194L CYS* 2.0 51.1 - - + -
196L VAL* 4.3 4.5 - - - -
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Residues in contact with LEU 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H LEU* 5.1 0.4 - - + -
174H PHE* 3.8 22.7 - - + -
188H SER* 3.9 18.8 - - - -
190H VAL* 3.1 36.3 - - + -
114L SER 3.5 1.6 - - - +
115L VAL* 3.3 4.9 - - - +
116L THR* 2.7 47.0 + - - +
118L PHE* 3.9 19.3 - - + -
133L VAL* 3.8 23.6 - - + -
134L CYS* 1.3 73.8 - - - +
136L ILE* 1.3 61.9 + - - +
137L SER* 5.3 0.6 + - - -
175L ALA 4.0 1.1 - - - -
176L SER* 3.5 23.8 - - - +
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Residues in contact with ILE 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H PHE* 3.6 4.6 - - - -
113L PRO* 3.5 30.1 - - + -
114L SER 3.3 4.3 - - - +
115L VAL* 4.2 3.4 - - + -
134L CYS* 4.2 13.2 - - - +
135L LEU* 1.3 79.3 - - - +
137L SER* 1.3 59.7 + - - +
139L PHE* 3.6 14.5 - - + -
144L VAL* 4.7 2.7 - - + -
146L VAL* 3.6 31.9 - - + -
161L THR* 5.8 0.2 - - + -
174L ALA* 3.2 3.8 - - - -
175L ALA* 2.9 54.2 + - + +
176L SER* 5.0 1.8 - - - +
177L SER 5.2 1.8 - - - +
196L VAL* 3.6 29.6 - - + -
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Residues in contact with SER 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H HIS* 4.0 19.1 - - - -
174H PHE* 4.1 7.1 - - - -
113L PRO* 3.4 2.3 - - - +
114L SER* 2.9 45.3 + - - -
135L LEU 5.3 0.7 + - - -
136L ILE* 1.3 75.1 - - - +
138L ASP* 1.3 75.9 + - - +
139L PHE* 3.3 4.5 + - - -
167L GLN* 3.4 14.1 - - - -
173L TYR 3.7 1.8 - - - -
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Residues in contact with ASP 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H HIS* 5.6 0.7 + - - -
111L ALA* 3.6 13.5 - - - +
112L ALA 3.5 13.6 - - - +
114L SER* 4.6 11.5 + - - +
137L SER* 1.3 85.7 + - - +
139L PHE* 1.3 59.4 + - - +
167L GLN* 3.0 35.8 + - - +
170L ASN* 3.2 15.1 + - - -
172L LYS* 3.6 19.1 + - + +
173L TYR 3.1 0.6 + - - -
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Residues in contact with PHE 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L ALA 3.1 11.2 - - - +
113L PRO* 3.8 17.5 - - + -
136L ILE* 3.6 36.8 - - + -
137L SER 3.9 6.7 - - - -
138L ASP* 1.3 80.0 - - - +
140L TYR* 1.3 64.3 + - - +
141L PRO 3.5 18.2 - - - -
142L GLY* 3.8 1.3 - - - -
143L ALA 3.8 14.1 - - - -
144L VAL* 3.6 25.6 - - + -
164L PRO* 3.9 15.9 - - + -
172L LYS* 3.5 1.8 - - - +
173L TYR* 2.9 63.8 + - + +
174L ALA* 3.7 4.9 - - - -
175L ALA* 3.9 6.7 - - + -
198L HIS* 3.8 6.5 - + + +
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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