Contacts of the helix formed by residues 322 - 327 (chain A) in PDB entry 1KCW
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 LEU 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A GLN* 2.9 17.0 + - - +
321A ASN* 1.3 73.0 + - - +
323A ASN* 1.3 68.3 + - - +
325A LEU* 2.9 20.9 + - + +
326A LYS* 3.1 15.4 + - - +
526A PRO* 4.0 18.2 - - + +
527A THR* 4.0 39.9 - - + +
530A ILE* 4.7 16.6 - - + -
531A PHE* 3.5 38.1 - - + -
630A ALA* 6.3 0.7 - - + -
631A GLY* 3.5 24.9 + - - +
632A ASN* 4.8 1.6 - - + +
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Residues in contact with ASN 323 (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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241A TYR* 4.7 1.9 - - + +
321A ASN* 3.0 4.1 + - - +
322A LEU* 1.3 78.1 - - - +
324A HIS* 1.3 65.8 + - + +
326A LYS* 3.6 27.4 + - - +
327A ALA* 3.2 23.9 + - - +
570A GLU* 5.5 0.3 - - - +
632A ASN* 3.8 22.1 + - - +
633A GLU* 3.7 32.3 + - - +
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Residues in contact with HIS 324 (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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204A VAL* 4.2 3.5 - - + +
241A TYR* 3.4 31.2 - + + -
273A VAL* 3.1 29.2 + - - +
275A VAL 3.5 6.3 - - - -
276A HIS* 3.4 14.9 + + - -
319A CYS* 3.9 5.4 - - - -
321A ASN* 3.2 31.6 + - - +
322A LEU 3.1 1.0 - - - -
323A ASN* 1.3 75.8 - - + +
325A LEU* 1.3 66.0 + - - +
327A ALA* 3.0 12.5 + - - +
328A GLY 3.2 7.4 + - - -
329A LEU* 3.4 21.6 + - + +
633A GLU* 3.7 10.9 + - - -
1049A CU 2.0 34.9 - - - -
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Residues in contact with LEU 325 (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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28A VAL* 3.6 32.1 - - + -
29A ASP 4.1 6.7 - - - +
30A THR* 5.1 0.3 + - - -
281A HIS* 5.9 0.4 - - + -
318A SER* 3.9 24.9 - - - +
319A CYS 3.9 9.3 + - - +
320A GLN* 4.5 11.4 - - - +
321A ASN 2.9 11.8 + - - +
322A LEU* 2.9 15.1 + - + +
324A HIS* 1.3 76.7 - - - +
326A LYS* 1.3 55.8 + - - +
328A GLY* 3.2 8.8 + - - -
329A LEU* 4.6 2.7 - - - +
330A GLN* 2.6 42.9 - - - +
526A PRO* 4.2 13.9 - - + -
527A THR* 3.8 22.9 - - + -
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Residues in contact with LYS 326 (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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29A ASP* 3.2 42.1 - - - +
30A THR* 4.7 3.0 + - - -
32A HIS* 3.3 35.0 + - + +
248A PHE* 5.2 1.9 - - - -
322A LEU 3.1 10.8 + - - +
323A ASN* 3.7 31.9 + - - +
325A LEU* 1.3 73.2 - - - +
327A ALA* 1.3 59.3 + - + +
328A GLY 2.9 7.7 + - - -
527A THR* 3.9 19.9 + - + +
570A GLU* 3.1 35.2 + - - -
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Residues in contact with ALA 327 (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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32A HIS* 5.6 0.2 - - - -
36A TYR* 3.5 42.0 - - - +
241A TYR* 3.5 36.1 - - + +
248A PHE* 3.7 8.9 - - - -
323A ASN 3.2 16.5 + - - +
324A HIS 3.0 4.9 + - - +
326A LYS* 1.3 77.2 - - + +
328A GLY* 1.3 63.3 + - - +
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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