Contacts of the helix formed by residues 370 - 385 (chain C) in PDB entry 1KRB
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 VAL 370 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ILE 5.8 0.9 - - - +
132C ASP* 3.6 15.3 - - + +
149C SER* 5.6 1.0 + - - -
151C VAL* 4.9 11.4 - - + -
299C ASN* 3.8 6.1 - - - +
302C LEU* 6.1 0.2 - - - +
357C THR* 3.9 35.1 - - - +
358C SER* 3.6 3.6 - - - +
359C SER* 3.5 42.2 - - - +
366C ARG 4.5 0.7 - - - +
367C VAL 4.6 6.0 + - - +
368C GLY 3.8 1.6 - - - -
369C GLU* 1.3 76.9 - - - +
371C ILE* 1.3 62.5 + - + +
373C ARG* 4.4 0.7 - - - +
374C THR* 2.7 34.1 + - - -
407C TYR* 4.2 13.2 - - + -
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Residues in contact with ILE 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLY* 4.9 0.2 - - - -
149C SER* 3.1 30.7 + - - +
150C GLY* 3.8 23.6 - - - +
151C VAL* 4.1 13.7 - - + -
368C GLY 5.4 0.6 + - - +
370C VAL* 1.3 74.5 - - + +
372C LEU* 1.3 67.0 + - - +
374C THR* 3.2 3.5 + - - -
375C TRP* 3.0 38.0 + - + +
407C TYR* 3.5 49.1 - - + +
435C TRP* 4.4 10.5 - - + -
440C PHE* 6.0 0.2 - - + -
441C GLY* 3.8 20.2 - - - +
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C GLY 4.7 5.1 + - - +
369C GLU* 4.0 35.9 - - + +
370C VAL 3.5 0.2 - - - -
371C ILE* 1.3 81.0 - - - +
373C ARG* 1.3 72.5 + - + +
375C TRP* 3.5 0.9 + - - -
376C GLN* 3.1 54.1 + - - +
441C GLY 3.7 19.5 + - - +
442C VAL* 5.1 3.8 - - + +
560C MET* 3.9 25.9 - - + +
565C PHE* 4.1 31.4 - - + -
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Residues in contact with ARG 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASN* 3.2 39.5 + - + -
300C PRO* 3.5 13.5 + - - -
302C LEU* 2.8 39.8 + - + +
303C PRO* 4.4 3.3 + - - +
305C THR* 6.2 0.8 - - - +
366C ARG* 3.5 29.2 - - - +
369C GLU* 2.8 46.1 + - - +
370C VAL 4.5 1.1 - - - +
372C LEU* 1.3 78.2 - - + +
374C THR* 1.3 65.3 + - - +
376C GLN* 3.1 20.1 + - - +
377C VAL* 3.0 27.7 + - - +
558C LEU* 6.3 0.6 - - - +
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Residues in contact with THR 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 5.3 1.4 - - - +
357C THR* 2.9 31.0 + - + +
370C VAL 2.7 23.5 + - - -
371C ILE 3.2 6.1 + - - -
373C ARG* 1.3 77.1 - - - +
375C TRP* 1.3 62.2 + - + +
377C VAL* 3.3 8.5 + - - +
378C ALA 3.1 16.3 + - - -
403C TYR* 3.5 47.9 - - + +
406C LYS* 4.4 5.6 - - + -
407C TYR* 4.0 15.2 - - + -
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Residues in contact with TRP 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.6 2.9 - - + -
26C THR* 4.9 1.8 - - - +
28C LEU* 4.0 13.8 - - + +
371C ILE* 3.0 35.0 + - + +
372C LEU* 4.8 0.2 - - - -
374C THR* 1.3 74.4 - - + +
376C GLN* 1.3 60.6 + - - +
378C ALA* 3.3 16.9 + - + +
379C HIS* 3.0 27.9 + - - +
400C VAL* 3.4 50.9 - - + -
403C TYR* 3.8 16.6 - - + -
404C ILE* 3.8 20.6 - - + -
407C TYR* 3.0 34.0 + + - -
440C PHE* 3.6 30.2 - + - -
441C GLY* 4.4 7.0 - - - -
560C MET* 3.7 27.4 - - + -
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Residues in contact with GLN 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C THR* 6.0 0.4 - - - -
303C PRO* 3.8 19.7 - - + +
372C LEU* 3.1 33.3 + - + +
373C ARG* 3.1 23.0 + - - +
375C TRP* 1.3 76.2 - - - +
377C VAL* 1.3 57.7 + - - +
379C HIS* 3.4 7.5 + - - +
380C ARG* 3.0 33.1 + - - +
558C LEU* 3.6 26.7 - - + +
559C PRO* 2.9 31.6 + - + +
560C MET* 3.7 18.1 + - - -
561C ALA* 4.5 4.2 - - - +
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Residues in contact with VAL 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 3.8 33.4 - - + -
303C PRO* 3.8 18.2 - - + -
346C ASP* 4.0 29.4 - - + +
349C HIS* 4.5 7.2 - - + +
373C ARG 3.0 20.1 + - - +
374C THR* 3.5 9.2 - - - +
375C TRP 3.2 0.2 - - - -
376C GLN* 1.3 73.2 - - - +
378C ALA* 1.3 65.1 + - - +
380C ARG* 3.3 2.4 + - - +
381C MET* 2.9 31.6 + - + +
403C TYR* 3.8 22.0 - - + +
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Residues in contact with ALA 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.9 18.7 - - + +
374C THR 3.1 12.7 + - - +
375C TRP* 3.3 16.8 + - + +
377C VAL* 1.3 77.3 - - - +
379C HIS* 1.3 61.3 + - - +
381C MET 3.4 0.5 + - - -
382C LYS* 3.0 23.6 + - - +
399C ARG* 3.7 13.7 - - + +
403C TYR* 3.7 34.2 - - + -
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Residues in contact with HIS 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASP 5.0 0.9 - - - -
26C THR* 3.5 14.6 - - + -
27C GLU* 3.1 48.5 + - + +
28C LEU* 4.2 10.2 - - - +
375C TRP 3.0 13.2 + - - +
376C GLN* 3.5 10.1 - - - +
378C ALA* 1.3 76.8 - - - +
380C ARG* 1.3 75.7 + - + +
382C LYS* 3.1 4.6 + - - +
383C VAL* 3.0 43.8 + - + +
557C VAL 5.7 1.6 + - - -
558C LEU* 5.6 0.2 - - - -
559C PRO* 3.5 35.2 - - + +
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Residues in contact with ARG 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C PRO* 4.3 11.9 - - + -
304C TYR 4.9 1.2 + - - +
346C ASP* 5.5 1.1 - - - +
376C GLN 3.0 19.2 + - - +
377C VAL* 3.3 5.6 + - - +
379C HIS* 1.3 88.5 + - + +
381C MET* 1.3 60.8 + - + +
383C VAL* 3.6 21.3 + - - +
384C GLN* 2.9 62.1 + - - +
553C GLU* 3.2 30.9 + - - +
554C PRO 4.0 2.2 + - - -
555C ALA* 3.2 35.0 - - + +
556C ASP* 5.4 3.6 + - - -
557C VAL 4.9 3.6 + - - -
558C LEU* 3.7 20.0 - - + -
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Residues in contact with MET 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ASP* 3.6 45.1 - - + +
347C VAL* 3.8 14.8 - - + -
350C ASP* 3.4 27.8 - - + +
377C VAL* 2.9 22.2 + - + +
378C ALA 3.9 2.5 - - - +
380C ARG* 1.3 76.7 - - + +
382C LYS* 1.3 58.6 + - - +
384C GLN* 3.2 34.3 - - + +
385C ARG* 2.7 46.9 + - + +
386C GLY 3.7 0.3 + - - -
399C ARG* 4.0 2.8 + - - -
403C TYR* 3.7 14.1 - - - +
552C SER* 4.1 12.3 - - - -
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Residues in contact with LYS 382 (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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27C GLU* 2.8 39.0 + - + +
28C LEU* 4.1 8.5 - - + -
29C TRP* 4.3 7.9 - - - -
378C ALA 3.0 13.3 + - - +
379C HIS 3.6 7.2 - - - +
381C MET* 1.3 76.4 - - - +
383C VAL* 1.3 63.6 + - + +
386C GLY* 2.8 31.6 + - - +
396C ASP* 2.9 34.8 + - - +
399C ARG* 3.5 25.7 - - - +
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Residues in contact with VAL 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLU* 4.5 13.9 - - + -
379C HIS* 3.0 46.1 + - + +
380C ARG* 3.7 25.4 - - - +
381C MET 3.3 0.2 - - - -
382C LYS* 1.3 80.0 - - + +
384C GLN* 1.3 60.9 + - + +
386C GLY 4.9 0.5 + - - -
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Residues in contact with GLN 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ASP* 5.6 0.4 + - - -
380C ARG* 2.9 54.3 + - - +
381C MET* 3.2 23.3 - - - +
383C VAL* 1.3 83.1 - - + +
385C ARG* 1.3 68.5 + - + +
386C GLY 3.7 0.4 - - - -
552C SER* 3.5 8.1 - - - -
553C GLU* 2.9 36.6 + - + +
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Residues in contact with ARG 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C VAL* 4.3 21.5 - - - +
350C ASP* 2.9 29.5 + - - +
351C LEU* 3.5 31.6 - - - +
381C MET* 2.7 36.2 + - - +
384C GLN* 1.3 83.8 - - + +
386C GLY* 1.3 63.8 + - - +
387C ALA 3.7 7.2 + - - +
388C LEU* 3.8 14.6 - - - +
399C ARG* 4.8 0.6 - - - +
551C THR 5.8 0.4 - - - -
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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
------------------------------------------------------------
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