Contacts of the strand formed by residues 432 - 437 (chain A) in PDB entry 3CX5
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 432 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.4 13.2 - - + +
167A THR* 4.4 1.1 - - + -
168A ALA* 3.5 38.4 - - + +
244A PHE* 3.8 9.0 - - + -
245A LEU 4.5 1.8 - - - +
247A SER 3.1 7.2 - - - +
263A LEU* 3.4 4.5 - - - +
264A ALA 2.7 34.7 + - - +
327A LEU* 5.2 0.4 - - + -
431A ILE* 1.3 73.4 - - - +
433A ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 4.5 1.1 - - - -
167A THR* 3.7 5.6 - - - +
247A SER 3.0 8.4 + - - +
248A GLU* 3.1 28.5 - - + +
249A VAL 3.0 25.1 + - - -
250A ARG* 5.3 2.0 - - + +
261A ILE* 4.4 7.2 - - + -
262A SER 3.6 9.6 - - - +
263A LEU* 4.2 10.3 - - + -
431A ILE* 3.7 30.3 - - + -
432A ALA* 1.3 80.1 - - - +
434A ALA* 1.3 69.2 + - - +
442A LEU* 4.2 23.3 - - + -
445A TYR* 3.9 9.4 - - + -
448A ILE* 3.7 26.7 - - + -
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Residues in contact with ALA 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 3.5 29.3 - - + +
163A HIS* 3.9 8.5 - - + -
164A LEU* 3.6 22.4 - - + +
249A VAL* 3.3 13.2 - - + -
261A ILE* 3.5 5.2 - - - +
262A SER 3.0 31.6 + - - +
433A ILE* 1.3 80.2 - - - +
435A GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 435 (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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160A VAL* 4.2 5.5 - - - +
249A VAL 3.4 6.9 + - - -
250A ARG* 4.7 1.2 - - - +
251A LEU* 2.8 34.9 + - - +
260A TRP 3.1 12.8 - - - -
261A ILE* 4.3 2.9 - - - -
434A ALA* 1.3 77.0 - - - +
436A THR* 1.3 59.3 + - - -
439A ILE* 3.6 17.9 - - - +
442A LEU* 5.4 2.9 - - - +
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Residues in contact with THR 436 (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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156A HIS* 4.1 7.4 - - + -
159A ARG* 3.2 36.4 + - - +
160A VAL* 3.4 22.9 - - + -
251A LEU* 2.8 28.5 + - - -
253A ASP* 4.4 0.7 - - - +
256A LEU* 4.2 3.3 - - + +
260A TRP* 3.0 48.9 + - + +
435A GLY* 1.3 75.0 - - - -
437A GLY* 1.3 66.8 + - - +
439A ILE* 3.5 6.8 - - - +
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Residues in contact with GLY 437 (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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251A LEU 3.5 3.8 + - - -
252A ARG* 3.4 7.6 - - - +
253A ASP* 2.9 37.6 + - - +
256A LEU* 4.0 12.8 - - - -
258A LYS 3.3 10.5 - - - -
260A TRP* 4.4 0.9 - - - -
436A THR* 1.3 80.8 + - - +
438A GLN* 1.3 60.7 + - - -
439A ILE 2.9 9.1 + - - -
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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
------------------------------------------------------------
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