Contacts of the helix formed by residues 421 - 438 (chain C) in PDB entry 7KHC
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 421 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390C PHE* 4.9 1.3 - - - -
402C ARG* 5.7 0.7 - - - -
417C SER* 5.3 6.1 - - - -
419C ILE* 3.3 6.0 + - - +
420C LEU* 1.3 78.7 - - - +
422C LYS* 1.3 64.9 + - - +
423C ASP* 3.6 16.0 + - - +
424C ASP* 2.8 42.3 + - - +
425C ILE 3.7 1.9 + - - -
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Residues in contact with LYS 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LEU* 3.5 57.0 + - + +
214C ASN* 5.3 1.2 - - - +
215C TYR* 3.5 26.7 + - - +
390C PHE* 4.6 15.9 - - + -
420C LEU 4.0 0.2 + - - -
421C SER* 1.3 74.0 - - - +
423C ASP* 1.3 66.6 + - - +
425C ILE* 3.0 20.3 + - + +
426C ILE* 3.0 16.1 + - - +
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Residues in contact with ASP 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C TYR* 4.7 5.4 + - - -
411C ARG* 5.3 3.1 - - - +
421C SER* 3.2 10.4 + - - +
422C LYS* 1.3 79.5 - - - +
424C ASP* 1.3 63.9 + - - +
426C ILE* 3.3 14.9 + - - +
427C ASP* 2.9 38.9 + - - +
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Residues in contact with ASP 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ILE* 6.0 0.2 - - - -
402C ARG* 3.7 24.4 + - - -
405C PHE* 4.2 18.2 - - + -
411C ARG* 3.3 29.2 + - - +
420C LEU* 3.5 12.9 - - + -
421C SER* 2.8 40.5 + - - +
423C ASP* 1.3 77.5 - - - +
425C ILE* 1.3 64.5 + - + +
427C ASP* 3.2 2.1 + - - +
428C VAL* 2.9 27.8 + - - +
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Residues in contact with ILE 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ILE* 5.2 5.6 - - + -
184C LEU* 4.6 17.5 - - + -
186C PHE* 3.9 29.2 - - + -
209C ILE* 4.9 12.8 - - + -
210C LEU* 5.3 4.7 - - + -
213C LEU* 4.7 25.6 - - + -
385C PHE* 6.3 0.4 - - + -
389C PHE* 6.4 0.4 - - + -
390C PHE* 5.3 2.0 - - + -
420C LEU* 3.6 33.7 - - + -
421C SER 4.5 1.1 - - - +
422C LYS* 3.0 10.3 + - - +
424C ASP* 1.3 77.6 - - + +
426C ILE* 1.3 65.5 + - + +
428C VAL* 3.1 8.7 + - - +
429C MET* 3.0 29.7 + - - +
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Residues in contact with ILE 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C LEU* 5.6 10.5 - - + -
213C LEU* 4.9 7.6 - - + -
215C TYR* 3.4 38.6 - - + +
223C LEU* 4.5 13.0 - - + -
224C PHE* 4.6 20.6 - - + -
422C LYS* 3.0 19.0 + - + +
423C ASP* 3.7 12.8 - - - +
424C ASP 3.2 0.2 - - - -
425C ILE* 1.3 78.1 - - + +
427C ASP* 1.3 61.3 + - - +
429C MET* 3.2 7.8 + - - +
430C LYS* 2.9 51.3 + - + +
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Residues in contact with ASP 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C LEU* 3.8 11.8 - - + +
411C ARG* 2.3 42.0 + - - +
423C ASP* 2.9 25.1 + - - +
424C ASP 3.6 1.6 - - - +
426C ILE* 1.3 79.0 - - - +
428C VAL* 1.3 62.6 + - - +
430C LYS* 3.2 21.0 + - - +
431C LYS* 2.9 24.3 + - - +
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Residues in contact with VAL 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL* 4.3 13.9 - - + -
157C PHE* 4.3 2.6 - - + -
174C ALA* 4.0 24.2 - - + -
176C ILE* 3.9 24.5 - - + -
186C PHE* 4.6 10.1 - - + -
405C PHE* 3.4 29.8 - - + -
409C LEU* 4.4 7.0 - - + -
424C ASP 2.9 19.2 + - - +
425C ILE* 3.1 9.6 + - - +
427C ASP* 1.3 75.7 - - - +
429C MET* 1.3 59.3 + - - +
431C LYS* 3.1 7.8 + - - +
432C LEU* 2.9 25.5 + - - +
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Residues in contact with MET 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C PHE* 3.6 44.9 - - + -
194C LEU* 4.2 13.9 - - + -
206C ALA* 5.0 8.3 - - + -
207C THR* 5.7 1.1 - - - -
210C LEU* 3.4 42.8 - - + -
224C PHE* 4.0 16.6 - - + -
347C ILE* 4.5 12.1 - - + -
425C ILE* 3.0 19.2 + - - +
426C ILE* 3.8 7.0 - - - +
428C VAL* 1.3 76.7 - - - +
430C LYS* 1.3 62.9 + - - +
432C LEU* 3.5 6.6 - - + +
433C ILE* 2.9 35.9 + - + +
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Residues in contact with LYS 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C LEU* 3.8 24.4 + - - +
224C PHE* 5.3 10.7 - - + +
426C ILE* 2.9 36.3 + - + +
427C ASP* 3.2 22.6 + - - +
429C MET* 1.3 78.0 - - - +
431C LYS* 1.3 58.3 + - - +
433C ILE* 3.3 7.1 + - - +
434C ASP* 2.9 37.0 + - - +
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Residues in contact with LYS 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C PHE* 3.8 28.4 - - + -
408C SER 2.8 28.1 + - - -
409C LEU* 3.7 20.1 - - + +
410C LEU* 3.9 16.0 - - - +
427C ASP 2.9 12.9 + - - +
428C VAL 3.1 7.6 + - - +
430C LYS* 1.3 74.8 - - - +
432C LEU* 1.3 63.7 + - - +
434C ASP* 3.2 12.6 + - + +
435C ILE* 2.9 42.1 + - + +
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Residues in contact with LEU 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C PHE* 4.4 9.6 - - + -
172C TYR* 4.2 12.2 - - + +
173C ASN* 3.8 15.7 - - - +
174C ALA* 3.6 31.9 - - + +
186C PHE* 3.9 22.2 - - + +
188C PHE* 4.5 8.9 - - + -
194C LEU* 3.4 40.2 - - + -
428C VAL 2.9 13.8 + - - +
429C MET* 3.2 9.8 + - + +
431C LYS* 1.3 78.9 - - - +
433C ILE* 1.3 57.3 + - - +
435C ILE* 3.4 5.7 + - + +
436C ARG* 2.9 27.9 + - - +
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Residues in contact with ILE 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C PHE* 5.0 5.4 - - + -
194C LEU* 4.4 16.6 - - + -
224C PHE* 4.1 16.8 - - + -
225C PHE* 6.5 1.6 - - + -
344C GLY 5.6 0.9 - - - +
346C TYR* 3.7 30.3 - - + -
347C ILE* 4.0 29.4 - - + -
429C MET* 2.9 22.8 + - + +
430C LYS* 4.0 4.7 - - - +
432C LEU* 1.3 74.5 - - - +
434C ASP* 1.3 60.4 + - - +
436C ARG* 3.2 5.9 + - - +
437C ASN* 2.6 46.7 + - - +
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Residues in contact with ASP 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LYS* 2.9 24.8 + - - +
431C LYS* 3.5 16.8 - - + +
433C ILE* 1.3 77.6 - - - +
435C ILE* 1.3 63.3 + - + +
437C ASN* 3.1 24.7 + - - +
438C GLY 3.1 8.7 + - - -
439C LYS* 3.4 46.2 + - - +
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Residues in contact with ILE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C PHE* 4.1 34.8 - - + -
172C TYR* 3.1 32.6 + - + -
431C LYS* 2.9 29.3 + - + +
432C LEU* 3.8 5.8 - - + +
434C ASP* 1.3 74.6 - - + +
436C ARG* 1.3 58.1 + - - +
438C GLY* 2.8 22.1 + - - +
440C GLY* 4.0 30.2 - - - +
441C GLU 3.6 20.2 - - - +
442C VAL* 4.0 15.0 - - + -
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Residues in contact with ARG 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL 5.0 10.5 + - - -
171C LEU* 6.4 0.2 - - - +
172C TYR* 3.5 20.4 + - + -
188C PHE* 3.4 40.2 - - + -
192C ASP* 3.7 29.9 + - - -
346C TYR* 3.3 33.4 + - + +
432C LEU 2.9 17.8 + - - +
433C ILE* 3.2 7.2 + - - +
435C ILE* 1.3 75.8 - - - +
437C ASN* 1.3 60.8 + - - +
438C GLY* 4.7 0.2 - - - -
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Residues in contact with ASN 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C LEU* 4.5 12.3 - - - +
342C ASP* 3.0 36.6 + - + +
343C HIS* 5.0 10.3 + - - +
344C GLY 4.7 0.2 + - - -
346C TYR* 3.7 19.2 - - - -
433C ILE* 2.6 32.8 + - - +
434C ASP* 3.1 22.1 + - - +
436C ARG* 1.3 82.1 + - - +
438C GLY* 1.3 56.5 + - - +
439C LYS* 3.7 11.1 - - + +
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Residues in contact with GLY 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C TYR* 5.6 2.9 - - - -
434C ASP 3.1 0.8 + - - -
435C ILE 2.8 15.8 + - - -
437C ASN* 1.3 79.0 - - - +
439C LYS* 1.3 56.2 + - - +
440C GLY 3.3 13.0 + - - +
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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