Contacts of the strand formed by residues 165 - 170 (chain B) in PDB entry 5UKM
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 THR 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B HIS* 3.5 10.7 + - - -
160B SER* 3.5 1.2 - - - -
161B SER 2.9 24.8 + - - +
163B ASP* 2.4 43.1 + - - +
164B THR* 1.3 86.1 - - - +
166B CYS* 1.3 71.1 + - - +
179B THR* 4.7 7.1 - - + +
180B PHE 3.5 9.9 - - - -
181B THR* 4.5 18.8 - - + -
183B HIS* 6.0 0.7 - - - -
187B VAL* 3.3 4.9 - - - +
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Residues in contact with CYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 4.5 1.1 - - - -
159B THR 3.1 12.1 - - - +
160B SER* 3.7 11.9 - - - -
165B THR* 1.3 77.1 - - - +
167B ALA* 1.3 65.8 + - - +
179B THR* 3.8 5.9 - - - +
180B PHE* 2.9 36.0 + - + +
183B HIS* 5.2 1.6 - - - -
187B VAL* 3.6 31.4 - - - -
190B LEU* 4.8 0.9 - - - -
199B PHE* 3.9 26.7 - - + -
201B SER* 4.0 17.9 - - - -
211B TRP* 4.8 2.7 - - - -
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 4.1 3.8 - - + -
158B VAL* 3.3 1.7 - - - +
159B THR* 2.9 32.4 + - - +
166B CYS* 1.3 79.9 - - - +
168B LEU* 1.3 59.5 + - - +
169B TRP* 3.2 22.9 - - - +
176B GLN* 3.7 29.8 - - + +
178B THR 3.3 13.2 - - - +
179B THR* 4.6 0.4 - - + +
180B PHE* 3.6 6.5 - - - -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 4.1 15.5 - - + -
156B GLN* 3.5 29.8 - - + +
157B ILE 3.5 20.6 - - - +
158B VAL* 4.0 19.3 - - + +
167B ALA* 1.3 71.4 - - - +
169B TRP* 1.3 63.0 + - - +
176B GLN* 3.7 2.6 - - - -
177B THR* 2.9 31.7 + - + -
178B THR* 3.0 26.5 + - - +
180B PHE* 3.6 16.7 - - + -
213B VAL* 3.7 27.6 - - + +
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Residues in contact with TRP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B CYS* 5.8 0.2 - - + -
139B LEU* 3.2 49.1 - - + -
140B ALA 3.4 26.7 - - - -
141B GLY* 3.8 2.0 - - - -
142B HIS* 3.7 18.2 - + - -
156B GLN* 3.6 27.0 + - - +
157B ILE* 2.8 29.8 + - + +
159B THR* 2.6 32.7 + - + +
167B ALA* 3.2 18.3 + - - +
168B LEU* 1.3 78.6 - - - +
170B ASP* 1.3 63.5 + - - +
171B ILE 4.0 0.7 - - - -
174B GLY 3.6 19.5 - - - -
175B GLN* 3.6 15.9 - - - -
176B GLN* 3.4 37.7 - - + -
177B THR* 4.2 3.1 - - - -
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Residues in contact with ASP 170 (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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155B ASN* 3.1 33.6 + - - +
156B GLN* 5.0 4.3 - - - +
169B TRP* 1.3 73.7 - - - +
171B ILE* 1.3 54.0 + - - +
172B GLU* 3.3 8.2 + - - +
173B THR* 3.5 34.3 + - - +
174B GLY* 2.7 35.5 + - - -
175B GLN 3.2 7.2 + - - +
177B THR* 3.8 15.2 + - - +
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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