Contacts of the strand formed by residues 205 - 208 (chain A) in PDB entry 1PCU
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 TRP 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ILE* 3.2 39.5 + - + +
202A HIS* 3.0 54.6 + + + +
204A SER* 1.3 77.5 - - - +
206A VAL* 1.3 62.6 + - - +
244A PHE* 3.6 39.9 - + - -
260A LEU* 4.0 27.1 - - + -
261A LEU 4.0 2.7 - - - -
262A HIS* 3.5 28.5 + + + -
406A HIS* 3.5 45.8 - - + -
407A ILE* 3.7 18.4 - - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 4.4 7.2 - - + -
198A ALA* 3.8 26.2 - - + -
199A VAL 3.4 12.3 - - - +
200A LEU* 4.1 19.7 - - + -
204A SER 4.6 0.4 - - - +
205A TRP* 1.3 78.2 - - - +
207A LEU* 1.3 60.8 + - - +
221A VAL* 4.3 17.7 - - + -
223A LEU* 5.3 0.2 - - + -
260A LEU* 3.7 4.1 - - - +
261A LEU* 2.7 58.8 + - + +
263A LEU* 4.0 26.9 - - + -
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Residues in contact with LEU 207 (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 ALA* 3.2 10.9 - - - +
199A VAL* 2.8 37.6 + - + +
201A ILE* 3.7 26.9 - - + -
205A TRP 4.4 0.4 + - - -
206A VAL* 1.3 72.4 - - - +
208A THR* 1.3 59.1 + - - +
258A ILE* 3.8 31.9 - - + -
259A ALA 3.6 3.1 - - - +
260A LEU* 3.6 27.1 - - + -
261A LEU* 4.9 0.4 - - - -
276A ILE* 4.5 2.0 - - + -
361A GLY 4.1 1.6 - - - +
374A LEU* 3.9 27.1 - - + -
377A LEU* 4.0 17.7 - - + -
396A VAL* 4.3 2.5 - - + -
403A ILE* 3.9 14.1 - - + -
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Residues in contact with THR 208 (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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187A LEU* 3.8 16.3 - - + +
196A CYS* 4.0 7.4 - - - +
197A GLY 2.7 24.2 + - - -
206A VAL 4.0 0.2 + - - -
207A LEU* 1.3 74.8 - - - +
209A ALA* 1.3 72.7 + - - +
212A CYS* 4.7 7.6 - - + -
213A MET 5.5 3.1 - - - +
258A ILE* 3.9 0.3 - - - -
259A ALA* 3.0 40.2 + - + +
261A LEU* 3.7 26.2 - - + -
360A SER 4.0 0.2 + - - -
361A GLY* 3.7 6.9 - - - -
377A LEU* 3.5 16.7 - - - +
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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