Contacts of the strand formed by residues 168 - 173 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 3.0 11.3 + - - +
114D VAL* 3.4 4.6 - - + +
115D VAL* 2.9 26.8 + - - +
144D LYS* 3.5 24.0 - - + +
146D VAL* 4.2 20.0 - - + -
161D ALA* 4.0 37.7 - - + +
164D ASP* 4.5 2.5 - - + -
166D ASP 3.4 15.3 - - - +
167D PRO* 1.3 75.2 - - - +
169D VAL* 1.3 77.0 + - - +
170D PHE* 3.7 5.9 + - + +
193D ILE* 4.5 6.5 - - + -
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D LEU* 4.3 24.9 - - + -
115D VAL* 3.4 8.3 - - + +
117D MET* 3.6 27.1 - - + -
137D PHE* 3.6 35.7 - - + -
143D LEU* 4.4 19.5 - - + -
144D LYS 2.9 14.3 + - - +
145D VAL* 3.5 3.8 - - + -
146D VAL 2.9 26.5 + - - +
168D VAL* 1.3 76.5 - - - +
170D PHE* 1.3 60.4 + - - +
171D LEU* 4.0 8.4 - - + +
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Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.7 14.6 - - + -
114D VAL* 4.1 11.7 - - + -
115D VAL 2.8 13.2 + - - +
116D ARG* 3.1 10.5 - - + -
117D MET* 2.9 26.6 + - - +
146D VAL* 3.5 30.1 - - + -
148D VAL* 3.6 23.6 - - + -
154D ALA 3.8 4.5 - - - -
157D LEU 3.8 6.1 - - - -
158D LEU* 3.6 46.2 - - + -
161D ALA* 4.5 9.0 - - + -
168D VAL* 3.7 2.4 + - + -
169D VAL* 1.3 71.4 - - - +
171D LEU* 1.3 61.9 + - - +
172D GLU* 3.3 34.9 + - + -
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D MET* 3.4 15.5 - - + -
119D SER* 3.8 27.4 - - - +
133D PRO* 4.4 12.1 - - + -
134D GLU* 3.8 26.9 - - + +
137D PHE* 4.4 10.3 - - + -
145D VAL* 3.7 25.8 - - + -
146D VAL 2.7 21.6 + - - +
147D ALA* 3.4 11.6 - - + -
148D VAL* 3.3 28.6 + - - +
169D VAL* 4.0 14.6 - - + +
170D PHE* 1.3 74.3 - - - +
172D GLU* 1.3 60.6 + - - +
173D PRO* 3.6 3.0 - - + +
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Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D MET* 4.7 3.1 - - - -
10D LEU* 3.5 21.5 - - + +
116D ARG* 2.7 43.9 + - - +
117D MET 2.9 13.2 + - - +
118D PRO* 3.0 4.9 - - - +
119D SER* 2.9 21.2 + - - -
148D VAL* 4.5 4.5 - - + -
170D PHE* 3.3 32.4 - - + -
171D LEU* 1.3 76.3 - - - +
173D PRO* 1.3 69.2 - - - +
174D LYS* 2.9 2.9 + - - -
177D TYR* 2.5 43.7 + - + +
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Residues in contact with PRO 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D MET* 4.4 7.5 - - - +
119D SER* 3.2 15.0 - - - +
147D ALA* 5.5 2.7 - - + -
148D VAL* 3.0 31.4 - - + +
171D LEU 3.6 6.5 - - - +
172D GLU* 1.3 79.1 - - - +
174D LYS* 1.3 59.7 + - - +
175D ARG* 3.2 4.3 - - + -
176D LEU* 2.9 39.3 + - + +
177D TYR* 3.6 3.5 + - - -
211D GLY* 3.7 4.7 - - - -
212D THR* 3.4 40.4 - - - +
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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