Contacts of the strand formed by residues 162 - 166 (chain B) in PDB entry 3UMO
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 ARG 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 5.1 5.3 - - - +
131B GLY* 3.4 23.2 + - - -
132B ALA 2.9 13.7 + - - +
133B ILE* 3.3 20.0 - - + +
134B LEU 2.8 27.5 + - - +
160B GLY 3.9 9.2 - - - +
161B ILE* 1.3 72.7 - - - +
163B CYS* 1.3 60.7 + - - +
182B GLU* 3.1 45.7 + - + +
220B ARG* 4.3 5.7 - - - +
266B LEU* 3.6 40.8 + - + +
267B ALA* 5.3 1.2 + - - +
269B ASN* 4.6 17.8 + - - +
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Residues in contact with CYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 3.4 15.3 - - - +
136B ILE* 4.6 9.2 - - + -
153B ILE* 4.1 16.6 - - + -
156B ALA* 4.0 23.3 - - - -
157B GLN* 4.1 9.9 - - + +
161B ILE* 3.6 19.4 + - - -
162B ARG* 1.3 74.3 - - - +
164B ILE* 1.3 62.9 + - - +
165B VAL* 5.1 0.4 - - + -
180B ASN 5.7 0.4 + - - -
181B ILE* 3.4 22.8 - - + +
182B GLU* 2.9 36.6 + - - +
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Residues in contact with ILE 164 (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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133B ILE* 3.8 24.5 - - + -
134B LEU 2.8 9.5 + - - +
135B VAL* 3.4 17.6 - - + -
136B ILE* 2.8 28.2 + - - +
162B ARG 5.4 0.2 - - - -
163B CYS* 1.3 78.3 - - - +
165B VAL* 1.3 71.3 + - - +
182B GLU* 4.6 5.4 - - + -
183B LEU* 3.3 43.1 - - + +
185B LYS* 6.0 0.9 - - + +
259B VAL* 4.5 9.0 - - + -
263B THR* 3.5 33.2 - - + +
266B LEU* 4.5 10.3 - - + -
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 5.8 0.2 - - - -
136B ILE* 3.5 23.3 - - + +
153B ILE* 4.7 0.4 - - + -
163B CYS 5.0 0.2 - - - -
164B ILE* 1.3 84.3 - - - +
166B ASP* 1.3 64.3 + - - +
167B SER* 4.3 6.5 - - - +
172B LEU* 3.7 27.1 - - + -
175B ALA* 3.8 25.4 - - + -
176B LEU* 5.6 1.8 - - + -
181B ILE* 3.9 34.1 - - + -
183B LEU 2.9 8.3 + - - +
184B VAL* 3.3 9.9 - - + +
185B LYS* 3.3 23.2 + - - +
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Residues in contact with ASP 166 (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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135B VAL* 5.6 0.6 - - + +
136B ILE 3.0 7.9 + - - +
137B SER* 3.2 22.3 + - - +
138B GLY 3.0 24.3 + - - -
164B ILE* 6.0 0.2 - - + -
165B VAL* 1.3 73.2 - - - +
167B SER* 1.3 67.0 + - - +
184B VAL* 5.4 0.7 - - - -
185B LYS* 3.5 31.6 - - + +
190B GLU* 4.2 3.8 - - - +
255B GLY 4.5 1.2 - - - +
256B ASP* 4.4 8.3 - - - +
259B VAL* 3.4 30.1 - - + +
311B MG 4.2 14.1 - - - -
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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