Contacts of the strand formed by residues 168 - 173 (chain B) in PDB entry 1UMD
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 VAL 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 3.1 10.0 + - - +
114B VAL* 3.4 5.4 - - + +
115B VAL* 2.9 27.2 + - - +
144B LYS* 3.4 22.0 - - + +
146B VAL* 4.2 20.2 - - + -
161B ALA* 3.9 39.5 - - + +
164B ASP* 4.4 7.6 - - + -
166B ASP 3.4 15.7 - - - +
167B PRO* 1.3 75.6 - - - +
169B VAL* 1.3 76.1 + - - +
170B PHE* 3.7 5.7 + - + +
193B ILE* 4.5 3.8 - - + -
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 4.3 16.4 - - + -
115B VAL* 3.5 9.2 - - + +
117B MET* 3.7 20.6 - - + -
137B PHE* 3.5 41.1 - - + -
143B LEU* 4.3 28.3 - - + -
144B LYS 2.9 14.7 + - - +
145B VAL* 3.5 4.8 - - + -
146B VAL 2.9 26.9 + - - +
168B VAL* 1.3 74.8 - - - +
170B PHE* 1.3 60.2 + - - +
171B LEU* 3.9 8.2 - - + +
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Residues in contact with PHE 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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10B LEU* 3.7 15.3 - - + -
114B VAL* 4.1 15.7 - - + -
115B VAL 2.8 13.3 + - - +
116B ARG* 3.4 4.4 - - + -
117B MET* 3.0 26.1 + - - +
146B VAL* 3.5 22.2 - - + -
148B VAL* 3.7 22.9 - - + -
154B ALA 3.7 5.2 - - - -
157B LEU* 3.7 15.7 - - + -
158B LEU* 3.5 48.7 - - + -
161B ALA* 4.5 8.3 - - + -
168B VAL* 3.7 2.0 + - + -
169B VAL* 1.3 71.0 - - - +
171B LEU* 1.3 61.9 + - - +
172B GLU* 3.4 34.2 + - + +
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Residues in contact with LEU 171 (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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117B MET* 3.4 16.8 - - + +
119B SER* 3.7 26.2 - - - +
133B PRO* 4.4 11.9 - - + -
134B GLU* 3.7 30.1 - - + +
137B PHE* 4.4 9.4 - - + -
145B VAL* 3.8 24.7 - - + -
146B VAL 2.7 23.1 + - - +
147B ALA* 3.4 11.9 - - + -
148B VAL* 3.3 26.7 + - - +
169B VAL* 3.9 15.9 - - + +
170B PHE* 1.3 75.0 - - - +
172B GLU* 1.3 63.4 + - - +
173B PRO* 3.6 2.9 - - + +
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Residues in contact with GLU 172 (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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6B MET* 4.7 4.0 - - - -
10B LEU* 3.5 21.6 - - + +
116B ARG* 2.7 43.4 + - - +
117B MET 2.9 14.5 + - - +
118B PRO* 3.1 4.5 - - - +
119B SER* 2.8 21.0 + - - -
148B VAL* 4.6 4.3 - - + -
170B PHE* 3.4 31.5 - - + +
171B LEU* 1.3 76.5 - - - +
173B PRO* 1.3 64.3 - - - +
174B LYS* 2.9 7.4 + - - -
177B TYR* 2.5 42.7 + - + +
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Residues in contact with PRO 173 (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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6B MET* 4.4 6.5 - - - +
119B SER* 3.2 15.7 - - - +
147B ALA* 5.5 2.5 - - + -
148B VAL* 3.0 30.5 - - + +
171B LEU* 3.6 6.3 - - + +
172B GLU* 1.3 79.4 - - - +
174B LYS* 1.3 60.0 + - - +
175B ARG* 3.2 4.0 - - + +
176B LEU* 2.9 38.6 + - + +
177B TYR* 3.6 3.2 + - - -
211B GLY* 3.7 5.4 - - - -
212B THR* 3.4 41.3 - - - +
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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