Contacts of the helix formed by residues 432 - 447 (chain B) in PDB entry 1K9A
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 THR 432 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLU* 3.9 20.9 - - - +
365B THR* 5.6 0.2 - - - -
366B LYS* 3.9 17.5 - - - +
369B VAL* 4.8 2.0 - - - -
431B PRO* 1.3 78.9 - - - +
433B PHE* 1.3 60.4 + - - +
434B LEU* 3.3 4.4 + - - +
435B GLN* 3.0 21.9 + - - +
436B LEU* 3.0 25.3 + - - +
306C GLU 5.0 1.8 - - - +
307C GLY* 2.9 34.6 + - - +
309C ASN* 4.4 14.1 - - - +
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Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B CYS* 3.7 12.6 - - - +
302B MET* 3.4 50.9 - - + -
303B GLU* 3.5 24.8 - - + +
306B GLU* 3.0 26.5 + - + +
365B THR* 3.6 22.2 - - + -
368B ASP* 3.9 14.1 - - + -
369B VAL* 3.7 24.9 - - + -
372B PHE* 4.0 15.0 - + + -
432B THR* 1.3 71.7 - - - +
434B LEU* 1.3 62.2 + - - +
436B LEU* 3.1 25.3 + - + +
437B ARG* 2.8 30.8 + - - +
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU* 3.5 20.3 + - + +
306B GLU* 4.6 0.8 + - - -
432B THR* 3.2 7.9 + - - +
433B PHE* 1.3 76.9 - - - +
435B GLN* 1.3 60.8 + - - +
437B ARG* 3.0 29.8 + - - +
438B GLU* 2.9 46.5 + - + +
303C GLU* 3.5 39.7 - - + +
304C TYR* 4.0 15.0 - - + -
307C GLY* 4.0 12.1 - - - -
308C ASN* 3.8 20.9 - - - +
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Residues in contact with GLN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PRO* 3.3 19.8 - - + +
432B THR* 3.0 39.2 + - - +
434B LEU* 1.3 75.9 - - - +
436B LEU* 1.3 65.5 + - - +
438B GLU* 3.3 6.7 + - - +
439B GLN* 3.0 24.0 + - - +
307C GLY 3.2 13.9 - - - +
308C ASN* 2.8 45.7 + - - +
309C ASN* 4.2 8.1 + - - +
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B CYS* 3.7 11.7 - - - -
369B VAL* 4.1 17.0 - - + -
372B PHE* 3.9 17.5 - - + -
418B VAL* 3.7 21.3 - - + +
421B ASN* 5.7 1.8 - - - +
422B CYS* 3.6 18.2 - - - -
431B PRO* 3.6 20.0 - - + -
432B THR 3.0 17.0 + - - +
433B PHE* 3.5 38.4 - - + +
435B GLN* 1.3 76.5 - - - +
437B ARG* 1.3 64.1 + - - +
439B GLN* 3.1 6.8 + - + +
440B LEU* 2.9 26.8 + - + +
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Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.5 8.3 - - + -
299B CYS* 3.5 15.0 - - - -
300B GLU* 4.0 23.1 - - + -
303B GLU* 3.1 39.3 + - - +
433B PHE 2.8 16.3 + - - +
434B LEU* 3.0 28.9 + - - +
436B LEU* 1.3 73.3 - - - +
438B GLU* 1.3 82.8 + - - +
440B LEU* 3.0 5.8 + - - +
441B GLU* 2.9 51.5 + - + +
245C HIS* 6.2 1.8 - - - -
303C GLU* 6.2 1.2 - - - -
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Residues in contact with GLU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 2.9 38.7 + - + +
435B GLN* 3.5 7.6 - - - +
436B LEU 3.3 0.2 - - - -
437B ARG* 1.3 98.2 + - - +
439B GLN* 1.3 57.1 + - - +
441B GLU* 3.4 14.7 + - - +
442B HIS* 2.9 27.1 + - - +
244C ARG 4.4 6.4 - - - +
245C HIS* 5.0 5.1 + - - -
304C TYR* 3.9 29.4 + - + -
308C ASN* 5.6 0.4 - - - +
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Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ALA* 5.5 3.0 + - - +
418B VAL* 3.9 26.0 - - + +
421B ASN* 6.3 1.1 - - - +
435B GLN 3.0 16.6 + - - +
436B LEU* 3.7 5.8 - - + +
438B GLU* 1.3 73.9 - - - +
440B LEU* 1.3 67.4 + - - +
442B HIS* 3.1 29.5 + - - +
443B ILE* 2.9 35.9 + - + +
10C SER 4.9 9.7 + - - -
11C GLY* 5.3 1.6 + - - -
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.1 23.2 - - + +
295B SER* 4.1 17.0 - - - +
296B LEU* 3.5 26.2 - - + -
299B CYS* 4.0 29.2 - - + -
372B PHE* 4.1 12.1 - - + -
376B LEU* 5.0 6.5 - - + -
415B VAL* 5.4 4.5 - - + -
418B VAL* 4.4 27.1 - - + -
436B LEU 2.9 18.5 + - - +
437B ARG 3.6 2.5 - - - +
439B GLN* 1.3 76.0 - - - +
441B GLU* 1.3 58.0 + - - +
443B ILE* 3.3 12.4 + - + +
444B ARG* 2.9 26.2 + - - +
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.1 14.1 - - + +
300B GLU* 5.5 1.7 - - - +
437B ARG* 2.9 43.6 + - - +
438B GLU* 3.7 20.5 - - - +
440B LEU* 1.3 74.1 - - - +
442B HIS* 1.3 60.1 + - - +
443B ILE 3.0 1.6 - - - -
444B ARG* 3.7 31.9 + - - +
445B THR* 2.7 38.0 + - - +
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Residues in contact with HIS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B GLU 2.9 16.4 + - - +
439B GLN* 3.4 35.2 - - - +
441B GLU* 1.3 75.5 - - - +
443B ILE* 1.3 62.3 + - - +
445B THR* 3.5 4.1 + - - -
446B HIS* 3.1 62.9 + + - +
448B LEU* 4.6 2.7 - - + -
11C GLY* 2.9 35.8 + - - -
13C GLU* 4.7 16.4 - - + +
37C THR* 4.9 1.3 - - - +
244C ARG* 4.8 10.0 + - - -
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Residues in contact with ILE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.2 5.6 - - + -
414B ALA* 3.8 40.8 - - + +
415B VAL* 4.1 11.7 - - + +
418B VAL* 3.9 15.3 - - + -
439B GLN* 2.9 28.7 + - + +
440B LEU* 3.3 15.9 - - + +
442B HIS* 1.3 75.5 - - - +
444B ARG* 1.3 55.3 + - - +
446B HIS 3.1 2.3 + - - -
447B GLU 2.7 31.7 + - - -
448B LEU* 3.1 22.7 + - + -
449B HIS* 3.8 33.4 - - + +
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Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ASP* 5.7 1.6 - - - +
292B LEU* 3.8 14.1 - - + -
293B LYS* 4.9 11.1 - - - +
296B LEU* 3.3 29.6 - - + +
440B LEU 2.9 14.2 + - - +
441B GLU* 3.7 33.1 + - - +
443B ILE* 1.3 75.0 - - - +
445B THR* 1.3 68.8 + - - +
447B GLU* 3.0 19.1 + - - +
449B HIS* 3.8 16.3 - - + +
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Residues in contact with THR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B GLU* 2.7 25.8 + - - +
442B HIS* 3.6 7.8 - - - +
444B ARG* 1.3 79.9 + - - +
446B HIS* 1.3 75.5 + - + +
447B GLU* 3.7 2.8 + - - +
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Residues in contact with HIS 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B HIS* 3.1 53.3 + + - +
443B ILE 3.1 2.4 + - - -
445B THR* 1.3 91.4 + - + +
447B GLU* 1.3 72.2 + - - +
448B LEU* 3.1 23.3 + - + +
13C GLU* 5.4 2.1 + - - -
37C THR* 3.6 30.7 + - + +
51C LYS* 2.9 31.6 + - + +
244C ARG* 6.1 0.2 + - - -
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Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A LYS* 3.4 23.9 + - - -
443B ILE 2.7 8.5 + - - -
444B ARG 3.0 12.7 + - - +
445B THR 4.9 2.7 - - - +
446B HIS* 1.3 81.2 - - - +
448B LEU* 1.3 55.3 + - - +
449B HIS* 2.9 22.2 + - + -
450B LEU* 3.0 42.4 + - + +
51C LYS* 3.5 17.0 + - - +
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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
------------------------------------------------------------
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