Contacts of the strand formed by residues 261 - 266 (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 SER 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ALA 3.5 3.2 + - - -
198A VAL* 3.9 2.5 - - - +
199A PHE* 3.0 30.4 + - - +
230A ILE* 4.0 6.3 - - - -
231A PRO* 3.4 17.1 - - - +
233A TYR* 4.2 7.2 - - - -
250A ALA* 3.8 26.2 + - - +
253A ARG* 3.0 29.9 + - - -
260A PRO* 1.3 76.9 + - - +
262A LEU* 1.3 61.8 + - - +
263A VAL* 4.0 1.6 - - - -
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Residues in contact with LEU 262 (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* 4.0 22.0 - - + -
183A TRP* 4.1 25.6 - - + -
187A ILE* 4.7 2.0 - - + -
199A PHE* 3.3 20.9 - - + +
201A ALA 5.1 0.2 - - - +
221A ILE* 3.4 36.3 - - + +
222A ALA* 4.3 3.7 - - - +
225A ALA* 3.7 32.5 - - + +
228A PHE* 4.8 4.0 - - + -
230A ILE* 4.1 8.0 - - + +
231A PRO 3.0 6.9 + - - +
232A GLY* 3.2 2.6 - - - -
233A TYR* 2.9 25.8 + - - +
261A SER* 1.3 73.5 - - - +
263A VAL* 1.3 64.7 + - - +
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Residues in contact with VAL 263 (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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198A VAL* 4.3 11.0 - - + -
199A PHE 2.9 12.0 + - - +
200A ILE* 3.3 11.6 - - + +
201A ALA* 2.8 25.8 + - - -
233A TYR* 3.8 19.3 - - + -
235A VAL* 3.9 4.9 - - + -
246A VAL* 3.8 24.2 - - + +
247A VAL* 4.2 10.8 - - + -
250A ALA* 4.1 21.5 - - + -
261A SER* 4.6 1.1 - - - -
262A LEU* 1.3 77.8 - - - +
264A GLU* 1.3 61.7 + - - +
265A LEU* 3.8 25.8 - - + -
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Residues in contact with GLU 264 (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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201A ALA* 3.9 7.0 - - + -
203A ASN* 2.8 35.0 + - + -
220A THR* 3.4 4.2 - - - +
221A ILE* 2.7 44.8 + - + -
222A ALA 3.0 14.1 + - - +
233A TYR 2.7 17.7 + - - +
234A LEU* 3.4 26.8 - - + +
235A VAL* 2.8 34.5 + - - +
262A LEU 4.1 0.8 + - - -
263A VAL* 1.3 71.4 - - - +
265A LEU* 1.3 61.7 + - - +
266A ARG* 3.6 10.8 - - + -
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Residues in contact with LEU 265 (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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76A ALA* 3.6 34.5 - - + +
80A ILE* 4.1 12.6 - - + -
200A ILE* 3.6 29.4 - - + -
201A ALA 2.8 12.6 + - - +
202A GLU* 3.8 1.9 - - + -
203A ASN 3.1 23.1 + - - -
235A VAL* 3.7 27.4 - - + -
237A GLY* 4.0 9.4 - - - -
243A SER* 3.7 23.1 - - - +
246A VAL* 5.8 0.2 - - + -
247A VAL* 4.5 4.5 - - + -
263A VAL* 3.8 14.4 - - + -
264A GLU* 1.3 71.0 - - - +
266A ARG* 1.3 64.0 + - - +
267A VAL* 3.3 4.5 + - - +
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Residues in contact with ARG 266 (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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15A PRO* 4.3 24.4 - - - +
203A ASN* 3.6 6.5 - - - -
205A PHE* 3.7 35.4 - - + -
220A THR* 6.3 0.6 - - - +
234A LEU* 3.8 21.3 - - + +
235A VAL 2.9 19.6 + - - +
236A ASP* 3.9 3.9 - - - +
237A GLY* 2.7 26.3 + - - +
238A MET* 3.5 6.4 + - - +
264A GLU* 3.6 25.1 - - - +
265A LEU* 1.3 69.8 - - - +
267A VAL* 1.3 60.2 + - - +
291A TRP* 4.2 23.3 - - + -
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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