Contacts of the strand formed by residues 362 - 366 (chain A) in PDB entry 1CX4
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLN* 4.1 5.5 + - - -
302A ILE* 3.4 11.2 - - - -
303A ALA* 3.7 3.1 - - - +
304A GLN* 3.0 25.2 + - - +
321A ILE* 3.3 8.0 - - - +
322A THR* 2.8 45.5 + - - +
324A LYS* 5.8 3.5 - - - -
361A ALA* 1.3 75.9 - - - +
363A ALA* 1.3 63.1 + - - +
364A HIS* 4.1 14.8 - - - -
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Residues in contact with ALA 363 (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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300A GLN* 3.6 0.9 - - - -
301A ILE* 2.7 34.1 + - + -
302A ILE* 3.1 29.7 + - + +
319A VAL* 3.9 10.8 - - + -
320A ARG 3.3 6.1 - - - -
321A ILE* 3.6 21.8 - - + -
348A PHE* 3.9 9.4 - - + -
362A SER* 1.3 76.4 - - - +
364A HIS* 1.3 60.2 + - - +
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Residues in contact with HIS 364 (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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298A GLY* 3.4 24.9 - - - +
299A GLU 3.2 5.2 - - - +
300A GLN* 3.6 44.3 + - + +
301A ILE* 4.3 5.4 - - - +
319A VAL* 3.5 3.6 - - - +
320A ARG* 2.9 40.9 + - + +
322A THR* 4.5 8.7 + - - +
362A SER* 4.1 14.9 - - - -
363A ALA* 1.3 76.5 + - - +
365A ALA* 1.3 65.2 + - - +
366A ILE* 5.2 0.9 - - + -
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Residues in contact with ALA 365 (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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295A TYR* 3.9 12.8 - - + -
296A ASN 3.6 20.2 - - - +
297A ASP* 4.1 0.3 - - - +
298A GLY* 2.9 25.8 + - - -
299A GLU 3.0 10.1 + - - +
301A ILE* 4.3 6.3 - - + +
318A GLU 3.9 4.0 - - - -
364A HIS* 1.3 75.7 - - - +
366A ILE* 1.3 61.3 + - - +
367A GLY 3.8 3.6 - - - +
369A VAL* 3.4 27.8 - - + -
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Residues in contact with ILE 366 (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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297A ASP* 3.7 6.3 - - - +
317A GLY* 4.9 0.9 - - - -
318A GLU* 2.9 64.5 + - + +
320A ARG* 3.7 38.4 - - + -
341A ARG* 6.2 0.7 - - + -
364A HIS* 4.6 0.7 - - + +
365A ALA* 1.3 74.4 - - - +
367A GLY* 1.3 65.2 + - - +
368A THR 4.0 0.7 + - - +
369A VAL* 4.1 0.9 - - - +
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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