Contacts of the strand formed by residues 197 - 203 (chain A) 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 ALA 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ALA* 4.6 6.5 - - + +
157A ALA* 3.7 18.6 - - + -
169A ALA 3.2 9.0 - - - +
190A ALA* 4.7 4.3 - - + -
195A ALA 2.8 9.7 + - - +
196A PRO* 1.3 74.5 - - - +
198A VAL* 1.3 65.2 + - - +
199A PHE* 3.7 28.7 - - + -
254A ALA* 4.1 1.0 - - - +
259A GLY 4.6 0.3 - - - +
260A PRO* 2.9 32.0 - - + +
261A SER 3.5 0.2 + - - -
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Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 4.2 8.7 - - + -
169A ALA 2.9 6.7 + - - -
170A VAL* 3.4 11.1 - - + -
171A CYS 2.8 27.0 + - - +
197A ALA* 1.3 77.0 - - - +
199A PHE* 1.3 63.4 + - - +
200A ILE* 3.7 25.1 + - + +
247A VAL* 4.7 6.1 - - + -
250A ALA* 3.7 47.8 - - + +
251A VAL* 3.8 14.8 - - + +
254A ALA* 4.3 2.2 - - + -
261A SER 3.9 7.0 - - - +
263A VAL* 4.3 9.0 - - + -
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Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 3.9 21.8 - - + -
153A ALA* 4.4 3.6 - - + -
154A ALA* 4.5 6.5 - - + -
171A CYS* 3.5 28.5 - - + -
173A PHE* 3.8 15.7 - + + -
187A ILE* 3.7 39.9 - - + -
190A ALA* 3.8 19.5 - - + -
197A ALA* 3.7 28.7 - - + -
198A VAL* 1.3 72.2 - - - +
200A ILE* 1.3 62.2 + - - +
230A ILE* 5.2 0.2 - - + -
260A PRO* 3.9 16.2 - - + -
261A SER 3.0 17.1 + - - +
262A LEU* 3.3 13.2 - - + +
263A VAL 2.9 24.9 + - - -
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.8 30.3 - - + -
170A VAL* 4.5 11.2 - - + -
171A CYS 2.7 12.4 + - - +
172A THR* 3.3 10.4 - - + -
173A PHE* 3.1 30.3 + - - -
198A VAL* 3.7 19.5 - - + +
199A PHE* 1.3 77.7 - - - +
201A ALA* 1.3 64.8 + - - +
202A GLU* 3.8 1.5 + - + +
247A VAL* 3.8 29.2 - - + -
263A VAL* 3.3 15.5 - - + +
265A LEU* 3.6 31.4 - - + -
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 3.3 25.9 - - + +
174A GLY 4.9 1.1 - - - +
178A THR* 4.9 0.4 - - + -
200A ILE* 1.3 72.3 - - - +
202A GLU* 1.3 62.1 + - - +
203A ASN 3.3 3.2 + - - +
221A ILE* 4.0 36.3 - - + -
262A LEU* 5.1 0.8 - - + +
263A VAL 2.8 13.2 + - - +
264A GLU* 4.3 5.6 - - + -
265A LEU* 2.8 34.0 + - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A HIS* 2.9 38.3 + - + +
76A ALA* 4.6 14.1 - - + -
77A GLN* 3.0 25.5 + - - +
80A ILE* 4.7 7.7 - - + +
94A TYR* 3.6 15.0 + - - +
97A ASP* 2.4 28.0 - - - +
100A LEU* 4.9 0.2 - - - +
172A THR* 3.5 20.5 - - - +
173A PHE 2.8 13.7 + - - +
174A GLY* 3.5 16.4 - - - -
175A ASP* 3.9 0.9 + - - +
200A ILE* 4.9 2.0 - - + +
201A ALA* 1.3 71.0 - - - +
203A ASN* 1.3 61.2 + - - +
204A ASN* 3.4 5.2 + - - -
265A LEU* 3.8 6.5 - - - -
267A VAL* 4.3 5.4 - - + -
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Residues in contact with ASN 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASP* 3.3 22.9 - - - +
201A ALA 3.3 1.5 - - - +
202A GLU* 1.3 70.9 - - - +
204A ASN* 1.3 58.2 + - - +
205A PHE* 2.8 47.7 + - - -
212A TYR* 4.2 12.4 - - - -
221A ILE* 4.0 16.2 - - + +
264A GLU* 2.8 34.4 + - + +
265A LEU 3.1 13.3 + - - +
266A ARG* 3.6 3.4 - - - +
267A VAL* 2.9 26.9 + - - +
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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