Contacts of the helix formed by residues 370 - 377 (chain D) in PDB entry 7KHI
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 LYS 370 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B ARG* 3.2 29.5 - - - +
194B GLN* 6.1 0.9 - - - -
196B THR* 5.4 2.0 + - - -
368D LEU 3.5 0.6 + - - -
369D PRO* 1.3 70.4 - - - +
371D LYS* 1.3 69.5 + - + +
373D ALA* 2.8 21.5 + - - +
374D LEU* 2.9 12.9 + - - +
409D TRP* 4.0 39.9 - - + +
412D LEU* 4.6 2.2 - - - +
441D LEU* 3.7 29.2 - - + +
442D ILE 3.0 22.7 + - - +
443D GLU* 2.9 32.9 - - - +
444D GLY 4.5 1.2 + - - -
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Residues in contact with LYS 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243C MET* 4.7 15.5 - - + -
369D PRO* 3.4 2.1 - - + +
370D LYS* 1.3 88.4 - - + +
372D MET* 1.3 62.4 + - - +
374D LEU* 3.3 12.8 + - + +
375D GLU* 3.0 24.8 + - - +
409D TRP* 5.4 7.6 - - + -
443D GLU* 5.1 4.9 + - - -
444D GLY* 4.3 21.6 + - - +
445D LYS* 4.3 32.1 - - - +
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Residues in contact with MET 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243C MET* 3.4 37.0 - - - -
1244C HIS 4.1 4.7 - - - +
1245C ALA* 4.1 14.8 - - + -
351D GLY* 4.3 1.8 - - - -
352D ARG 4.1 18.6 - - - +
353D SER* 4.2 6.3 - - - -
368D LEU* 4.7 4.5 - - + -
369D PRO* 3.4 39.6 + - + +
370D LYS 3.2 0.2 - - - -
371D LYS* 1.3 80.1 - - - +
373D ALA* 1.3 56.4 + - - +
375D GLU* 3.3 1.4 + - - +
376D LEU* 2.9 41.1 + - + +
447D ILE* 4.0 15.5 - - + -
468D VAL* 3.8 28.5 - - + -
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Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D LEU* 3.3 25.1 - - + +
369D PRO 3.2 1.8 + - - -
370D LYS 2.8 15.6 + - - +
372D MET* 1.3 73.0 - - - +
374D LEU* 1.3 64.8 + - - +
376D LEU* 4.4 0.7 - - - -
377D PHE* 2.9 46.5 + - + +
412D LEU* 3.8 9.4 - - + -
416D ILE* 4.5 4.5 - - + -
441D LEU* 3.6 17.7 - - + -
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Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D LYS 2.9 10.9 + - - +
371D LYS* 3.6 14.6 - - + +
372D MET 3.3 0.2 - - - -
373D ALA* 1.3 75.9 - - - +
375D GLU* 1.3 69.0 + - - +
378D LYS* 3.0 26.2 + - + +
381D ILE* 3.4 24.5 - - + -
401D VAL* 3.7 36.8 - - + +
404D GLU* 5.0 8.5 - - + -
408D VAL* 4.3 11.7 - - + -
409D TRP* 4.3 20.9 - - + -
412D LEU* 3.5 13.6 - - + +
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Residues in contact with GLU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C ASN* 5.5 5.0 + - - -
1245C ALA* 3.9 34.3 - - + +
1246C ARG 4.3 1.3 - - - +
1247C SER* 3.3 27.5 + - - +
1265C PHE* 4.1 22.4 - - - -
371D LYS 3.0 17.1 + - - +
372D MET 3.7 2.7 - - - +
374D LEU* 1.3 85.1 - - - +
376D LEU* 1.3 66.1 + - - +
378D LYS* 3.4 31.9 + - - +
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Residues in contact with LEU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245C ALA* 4.5 8.3 - - + +
1246C ARG 4.2 3.8 - - - +
1247C SER* 3.9 4.7 - - - +
349D TYR* 3.7 49.7 - - - +
350D SER 3.8 17.3 - - - +
351D GLY 4.3 1.1 - - - +
368D LEU* 4.8 8.1 - - + -
372D MET* 2.9 34.5 + - + +
373D ALA* 4.4 1.1 - - - -
375D GLU* 1.3 76.6 - - - +
377D PHE* 1.3 77.6 + - + +
378D LYS 3.2 3.3 + - - -
379D PRO* 3.6 10.7 - - - +
421D VAL* 5.9 0.2 - - + -
468D VAL* 4.3 21.3 - - + +
470D VAL* 4.0 20.0 - - + -
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Residues in contact with PHE 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D LEU* 5.2 3.6 - - + -
373D ALA* 2.9 38.8 + - + +
374D LEU 3.7 1.3 - - - -
376D LEU* 1.3 89.6 - - + +
378D LYS* 1.3 65.9 + - - +
379D PRO* 3.2 4.5 - - - -
380D PHE* 3.0 33.5 + + + -
381D ILE* 2.9 28.3 + - + +
412D LEU* 5.3 1.3 - - + -
415D VAL* 4.8 8.7 - - + -
416D ILE* 3.2 36.3 - - + -
419D HIS* 3.1 32.1 - + + -
421D VAL* 3.9 26.7 - - + -
439D PRO* 5.4 0.7 - - + -
470D VAL* 4.3 8.1 - - + -
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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