Contacts of the strand formed by residues 269 - 273 (chain A) in PDB entry 3O75
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 GLN 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 4.0 14.5 + - + +
177A SER* 3.6 32.0 + - - +
179A PRO* 5.6 2.7 - - + -
241A ASP 2.9 21.2 + - - +
242A ALA* 3.1 12.7 - - + +
243A LEU 2.8 28.1 + - - +
267A GLN* 5.2 8.4 + - - +
268A LEU* 1.3 72.5 - - - +
270A LEU* 1.3 59.9 + - - +
328A ILE* 3.3 41.9 - - - +
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.0 3.6 - - - -
243A LEU* 3.6 42.0 - - + +
245A THR* 6.0 0.2 - - + -
251A LEU* 4.0 17.7 - - + -
254A VAL* 5.0 2.5 - - + -
255A PHE* 3.9 28.3 - - + -
258A LEU* 5.0 3.1 - - + -
268A LEU* 3.4 24.5 + - + +
269A GLN* 1.3 72.7 - - - +
271A GLY* 1.3 60.5 + - - +
284A LEU* 4.0 20.2 - - + -
285A PRO 4.5 3.3 + - - +
286A VAL* 3.7 21.6 - - + -
287A ASN* 3.1 23.2 + - - +
328A ILE* 3.6 13.3 - - - +
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Residues in contact with GLY 271 (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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170A LEU* 4.0 17.3 - - - -
174A LEU* 3.5 13.9 - - - +
243A LEU 2.8 11.5 + - - +
244A VAL* 3.1 6.0 - - - -
245A THR* 2.9 23.9 + - - +
270A LEU* 1.3 78.1 - - - +
272A THR* 1.3 62.2 + - - -
286A VAL* 4.8 0.4 - - - -
287A ASN 3.3 8.3 - - - -
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Residues in contact with THR 272 (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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170A LEU* 3.5 9.0 - - - +
245A THR* 2.6 27.7 + - - -
247A SER 3.8 5.9 + - - -
248A TYR* 3.9 3.6 - - + -
251A LEU* 3.6 28.1 - - + +
271A GLY* 1.3 73.4 - - - -
273A PHE* 1.3 78.8 + - - +
274A GLY 3.8 9.9 - - - +
279A LEU* 4.3 5.4 - - + -
286A VAL* 3.9 8.5 - - + -
287A ASN 2.9 14.7 + - - +
288A ALA* 3.3 5.1 - - + -
289A MET 3.0 24.1 + - - -
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Residues in contact with PHE 273 (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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1A F1X 3.7 6.3 - - - +
163A ASP* 3.7 15.3 - - - -
166A ALA* 3.8 7.2 - - + -
167A SER* 3.6 42.6 - - - -
170A LEU* 4.0 12.6 - - + -
197A ARG* 3.6 29.8 - - + -
244A VAL* 5.2 1.8 - - + -
245A THR 2.8 16.6 + - - -
246A THR* 3.3 31.0 - - + +
248A TYR* 3.0 15.6 + - - -
272A THR* 1.3 92.0 + - - +
274A GLY* 1.3 59.5 + - - +
289A MET* 3.9 5.2 - - + +
322A ARG* 3.2 43.3 - - - -
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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