Contacts of the helix formed by residues 397 - 409 (chain A) in PDB entry 1CK7
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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LEU* 4.0 9.9 - - + -
140A VAL* 3.8 31.4 - - + -
143A ALA* 4.3 13.5 - - + -
144A PHE* 3.5 40.2 - - + -
173A PHE* 3.6 24.7 - - + -
207A PHE* 3.7 20.9 - - + -
213A TRP* 3.7 22.0 - - + -
214A THR 3.4 8.0 + - - +
215A LEU* 5.0 3.0 - - + +
395A TYR 3.4 1.8 + - - -
396A SER* 1.3 70.5 + - - +
398A PHE* 1.3 56.8 + - - +
401A ALA* 2.4 40.3 + - - +
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Residues in contact with PHE 398 (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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143A ALA* 4.2 14.8 - - + +
146A ARG* 3.5 68.2 - - + +
147A ALA* 3.8 6.2 - - - +
150A VAL* 4.0 12.6 - - + -
215A LEU* 5.3 3.9 - - + +
396A SER* 2.9 8.3 + - - +
397A LEU* 1.3 79.4 - - - +
399A LEU* 1.3 110.2 + - + +
401A ALA* 3.5 1.4 - - - +
402A ALA* 2.9 19.8 + - + +
431A PHE* 3.9 27.6 - + + -
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Residues in contact with LEU 399 (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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396A SER* 2.8 23.8 + - - +
398A PHE* 1.3 115.0 - - + +
400A VAL* 1.3 65.8 + - - +
402A ALA* 2.7 13.5 + - + +
403A HIS* 3.0 12.7 + - - +
420A LEU* 4.6 8.1 - - + +
425A TYR* 4.5 11.0 - - + +
426A THR 3.8 18.2 - - - +
427A TYR* 4.2 13.5 - - + -
428A THR* 3.7 28.7 - - - +
431A PHE* 3.8 26.9 - - + -
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Residues in contact with VAL 400 (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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191A LEU* 4.1 13.7 - - + -
192A ALA* 3.8 29.2 - - + +
207A PHE* 3.9 4.3 - - + -
213A TRP* 3.4 28.9 - - + -
395A TYR* 4.2 0.9 - - + -
396A SER 3.1 18.9 + - - +
397A LEU 3.9 0.9 - - - +
399A LEU* 1.3 74.3 - - - +
401A ALA* 1.3 63.2 + - - +
403A HIS* 3.5 7.3 + - + +
404A ALA* 3.0 22.1 + - + +
425A TYR* 3.9 28.0 - - + -
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Residues in contact with ALA 401 (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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143A ALA 4.6 0.2 - - - +
144A PHE* 3.6 31.2 - - + -
147A ALA* 3.6 14.1 - - + -
207A PHE* 3.6 12.4 - - + -
397A LEU 2.4 23.6 + - - +
398A PHE* 3.5 3.6 - - - +
399A LEU 2.8 0.8 + - - -
400A VAL* 1.3 73.9 - - - +
402A ALA* 1.3 54.2 + - - +
404A ALA* 2.9 2.1 + - - +
405A PHE* 2.7 44.2 + - + -
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Residues in contact with ALA 402 (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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147A ALA* 3.3 16.7 - - + +
150A VAL* 3.8 35.9 - - + -
151A TRP* 2.9 23.3 + - - +
398A PHE* 2.9 14.4 + - + +
399A LEU* 2.7 15.5 + - - +
401A ALA* 1.3 72.2 - - - +
403A HIS* 1.3 61.7 + - - +
405A PHE* 3.3 1.5 + - - -
406A GLY 3.2 4.0 + - - -
420A LEU* 3.8 12.1 - - + -
431A PHE* 5.1 1.8 - - + -
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Residues in contact with HIS 403 (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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102A CYS* 3.8 12.9 - - + +
399A LEU 3.0 9.3 + - - +
400A VAL* 3.8 11.2 - - + +
402A ALA* 1.3 79.9 - - - +
404A ALA* 1.3 66.5 + - - +
406A GLY 3.3 0.7 + - - -
407A HIS* 3.6 5.6 + + - -
413A HIS* 3.9 0.9 - + - -
420A LEU* 2.8 40.8 + - + +
421A MET* 3.1 38.1 - - + +
422A ALA 2.9 25.9 + - - -
423A PRO 4.6 1.1 - - - -
990A ZN 2.3 35.8 - - - -
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Residues in contact with ALA 404 (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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102A CYS* 5.8 1.3 - - - -
192A ALA* 5.1 9.2 - - + -
193A HIS* 5.3 1.1 - - - +
194A ALA* 3.3 23.2 - - + +
205A SER* 4.5 2.0 - - - +
206A HIS 5.8 0.2 - - - +
207A PHE* 4.3 18.6 - - + -
400A VAL* 3.0 17.8 + - + +
401A ALA 2.9 4.1 + - - +
403A HIS* 1.3 84.4 - - + +
405A PHE* 1.3 60.0 + - + +
407A HIS* 2.7 34.8 + - - +
408A ALA 3.1 3.8 + - - -
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Residues in contact with PHE 405 (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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144A PHE* 3.8 30.3 - + - -
147A ALA* 3.8 17.9 - - + -
148A PHE* 3.2 50.5 - + + -
151A TRP* 3.8 15.9 - - + +
169A ILE* 4.6 1.6 - - + -
171A ILE* 3.8 20.6 - - + -
205A SER* 3.3 34.1 - - - -
207A PHE* 4.4 3.1 - + - -
401A ALA* 2.7 23.7 + - + +
402A ALA 3.5 5.8 - - - +
404A ALA* 1.3 78.4 - - + +
406A GLY* 1.3 54.5 + - - +
408A ALA* 3.1 10.3 + - + +
409A MET* 3.0 31.5 + - + +
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Residues in contact with GLY 406 (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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151A TRP* 3.5 18.1 - - - +
402A ALA 3.2 8.9 + - - -
403A HIS 3.3 0.4 + - - -
404A ALA 3.1 0.8 - - - -
405A PHE* 1.3 73.3 - - - +
407A HIS* 1.3 64.2 + - - +
409A MET* 3.2 6.0 + - - -
411A LEU* 2.8 40.9 + - - +
421A MET* 3.5 19.5 - - - -
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Residues in contact with HIS 407 (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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102A CYS* 4.1 1.1 - - - -
104A ASN* 3.4 35.0 + - + -
105A PRO 5.6 0.2 - - - -
194A ALA* 3.7 16.4 - - + +
195A PHE 4.7 0.9 - - - -
196A ALA* 3.8 15.2 - - - +
403A HIS* 3.6 17.6 + + - -
404A ALA* 2.7 16.1 + - - +
406A GLY* 1.3 79.2 - - - +
408A ALA* 1.3 59.7 + - - +
410A GLY* 3.1 15.1 + - - -
411A LEU 3.3 17.6 + - - +
412A GLU* 4.2 15.9 + - - -
413A HIS* 4.2 8.3 - + - -
421A MET* 3.7 13.8 - - + +
990A ZN 2.2 36.2 - - - -
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Residues in contact with ALA 408 (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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119A TRP* 2.4 32.9 + - - -
169A ILE* 3.6 17.0 - - + -
194A ALA* 4.8 1.1 - - + -
195A PHE 4.0 12.1 - - - -
197A PRO* 3.0 9.6 - - - +
203A GLY 3.2 26.2 - - - +
205A SER* 4.3 3.8 - - - +
404A ALA 3.1 3.0 + - - +
405A PHE* 3.1 19.2 + - - +
407A HIS* 1.3 81.0 - - - +
409A MET* 1.3 50.1 + - + +
410A GLY 3.2 0.2 - - - -
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Residues in contact with MET 409 (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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117A PRO 4.1 0.9 - - - +
119A TRP* 3.3 22.7 - - + -
124A ILE* 4.8 0.9 - - - -
148A PHE* 4.3 7.4 - - + -
151A TRP* 5.1 6.5 - - + -
157A LEU* 4.3 10.8 - - + -
159A PHE* 3.1 44.4 - - + -
169A ILE* 3.4 21.5 - - + -
197A PRO* 3.4 5.0 - - - +
405A PHE* 3.0 26.8 + - + +
406A GLY 3.2 7.2 + - - +
407A HIS 3.2 0.8 - - - -
408A ALA* 1.3 77.2 - - + +
410A GLY* 1.3 57.4 + - - +
411A LEU* 3.5 0.9 - - + -
441A ILE* 3.5 33.4 - - + -
444A LEU* 3.6 5.0 - - - +
445A TYR* 3.2 28.1 + - + -
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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
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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