Contacts of the strand formed by residues 131 - 136 (chain G) in PDB entry 3WUW
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 HIS 131 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G PHE* 3.6 4.9 - - - +
130G GLU* 1.3 112.4 + - + +
132G PHE* 1.3 64.6 - - - +
133G PHE* 4.0 10.8 - + + -
145G ARG* 2.9 44.8 + - + -
146G LEU 3.5 3.1 - - - +
147G VAL* 3.7 30.6 - - + +
148G GLY 4.2 0.9 - - - +
176G GLY* 3.3 4.7 - - - -
177G SER* 2.9 43.7 + - - +
182G PRO* 5.9 6.0 - - + +
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Residues in contact with PHE 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G PRO* 4.3 5.2 - - + -
123G CYS* 3.3 33.0 - - + -
124G TRP* 4.1 8.7 - - - -
125G SER 4.2 0.9 - - - -
129G PHE* 3.8 27.1 - + + -
131G HIS* 1.3 73.5 - - - +
133G PHE* 1.3 65.5 + - - +
145G ARG* 3.3 5.9 - - - +
146G LEU 2.9 31.7 + - - -
148G GLY* 3.8 16.2 - - - -
155G SER* 3.3 34.8 - - - -
156G LYS* 3.4 23.8 - - - -
157G ALA* 3.8 29.6 - - + -
159G PHE* 3.7 10.2 - - + -
175G TYR 3.3 10.3 - - - -
176G GLY* 4.3 1.3 - - - -
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Residues in contact with PHE 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G MET* 3.8 33.4 - - + -
131G HIS* 4.0 10.1 - + + -
132G PHE* 1.3 76.6 - - - +
134G LEU* 1.3 59.8 + - - +
143G PRO* 4.3 14.6 - - + -
144G SER 3.2 5.2 - - - +
145G ARG* 3.6 40.6 - - + -
159G PHE* 4.1 2.9 - - - -
174G CYS* 3.1 7.3 - - - +
175G TYR* 2.8 48.7 + - + +
177G SER* 3.3 30.7 - - - -
182G PRO 4.0 16.2 - - - -
185G LEU* 4.0 24.5 - - + -
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G LEU* 4.1 19.5 - - + -
121G LEU* 3.9 26.2 - - + -
133G PHE* 1.3 73.2 - - - +
135G HIS* 1.3 60.0 + - - +
143G PRO* 3.2 5.1 - - - +
144G SER* 2.9 35.4 + - - +
159G PHE* 3.6 48.6 - - + -
161G ILE* 4.1 11.4 - - + -
172G TYR* 3.8 27.4 - - + -
173G ARG 3.7 15.9 - - - +
174G CYS* 4.2 3.8 - - + -
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Residues in contact with HIS 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G SER* 4.1 11.5 + - - -
17G VAL* 4.0 32.6 - - + +
134G LEU* 1.3 77.1 - - - +
136G LYS* 1.3 75.9 + - - +
137G GLU* 3.8 2.4 + - - -
138G GLY 5.0 4.5 - - - -
139G ILE* 3.5 22.8 + - + -
141G LYS 3.9 18.0 + - - -
143G PRO* 4.2 19.7 - - + -
172G TYR* 3.5 3.7 - - - -
173G ARG* 2.9 35.2 + - - +
175G TYR* 4.0 25.0 + - + -
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Residues in contact with LYS 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 4.6 8.1 + - - -
79A ARG* 6.2 0.4 - - - +
135G HIS* 1.3 83.8 + - - +
137G GLU* 1.3 74.5 + - - +
138G GLY 3.4 0.5 + - - -
139G ILE* 2.9 53.4 + - + +
166G LEU 4.2 1.4 + - - -
167G ALA* 2.9 27.0 + - - +
168G LEU 4.1 0.9 - - - +
169G ALA 2.6 28.8 + - - +
170G GLY* 4.5 2.2 - - - -
171G THR 3.5 15.7 - - - +
172G TYR* 3.8 41.8 - - + +
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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