Contacts of the strand formed by residues 134 - 139 (chain B) in PDB entry 5UWS
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 ILE 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A MET* 3.5 27.2 - - + +
180A PRO 3.6 16.4 - - - +
181A ALA* 3.6 32.1 - - + -
125B LEU* 4.0 8.7 - - + -
126B MET 3.6 6.7 - - - +
127B ARG* 3.4 26.0 - - + +
128B ARG* 4.9 5.6 + - - -
133B LYS* 1.3 73.6 - - - +
135B CYS* 1.3 61.4 + - - +
136B ALA 3.5 25.4 - - - +
137B ASN* 4.0 6.1 - - + +
165B ALA* 3.5 29.8 - - + +
166B GLU* 5.3 2.1 - - - +
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Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 3.0 19.5 - - + +
106B ARG* 3.1 44.9 + - + +
107B GLY* 3.9 18.6 - - - -
126B MET* 3.0 45.8 + - - -
127B ARG 4.2 2.5 - - - -
128B ARG* 3.9 17.3 - - - +
133B LYS 3.4 0.4 + - - -
134B ILE* 1.3 72.8 - - - +
136B ALA* 1.3 59.2 + - - +
165B ALA* 3.7 7.6 - - - -
166B GLU* 6.1 0.4 - - - -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 3.6 17.3 - - + -
106B ARG* 5.0 0.7 - - - +
124B ILE* 3.8 14.6 - - + -
125B LEU* 3.4 4.0 - - - -
126B MET* 3.0 40.9 + - + -
134B ILE* 3.5 4.9 - - - +
135B CYS* 1.3 81.7 - - - +
137B ASN* 1.3 63.9 + - - +
138B HIS* 4.3 7.9 - - + -
163B ASP* 3.5 10.3 - - - +
165B ALA* 3.6 3.7 - - - +
174B PHE* 5.4 0.7 - - + -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ALA* 4.1 2.4 - - - +
182A LEU 2.6 33.1 + - - +
184A PRO* 3.4 5.2 - - - +
123B ARG* 3.0 32.0 + - - +
124B ILE 3.2 4.5 - - - -
125B LEU* 3.7 11.4 - - + +
134B ILE* 4.0 10.7 - - + +
136B ALA* 1.3 75.4 - - - +
138B HIS* 1.3 64.8 + - - +
163B ASP* 2.7 17.3 + - - +
164B ILE* 3.1 39.5 + - + +
165B ALA* 4.2 4.2 - - - +
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Residues in contact with HIS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PRO* 3.6 14.8 - - - -
93B LEU* 6.3 0.4 - - + -
123B ARG* 3.4 0.3 - - - +
124B ILE* 2.8 56.7 + - + +
136B ALA* 4.3 7.6 - - + -
137B ASN* 1.3 78.0 + - - +
139B ILE* 1.3 76.9 + - - +
140B ILE* 4.8 1.1 - - - -
144B TYR* 4.6 5.4 - + - +
158B TYR* 3.1 29.0 + + - -
160B CYS* 3.6 19.0 - - - -
162B ALA 3.3 19.3 - - - +
163B ASP* 2.8 22.1 + - - +
174B PHE* 3.8 17.7 - + - -
191B PHE* 6.3 0.2 - + - -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PRO* 3.7 30.0 - - + +
185A PRO 3.5 27.4 + - - +
186A GLU* 4.0 22.7 - - + +
121B LYS* 4.0 26.2 - - + -
122B VAL 3.5 17.9 - - - +
123B ARG* 4.1 6.1 - - + +
138B HIS* 1.3 79.2 - - - +
140B ILE* 1.3 69.3 + - - +
141B ALA* 2.9 16.4 + - + +
142B PRO* 5.8 0.4 - - + -
144B TYR* 3.5 16.8 + - - -
162B ALA 4.9 0.2 + - - -
198B ASN* 3.7 13.7 - - + +
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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