Contacts of the helix formed by residues 444 - 451 (chain A) in PDB entry 1KB9
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 ASP 444 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A GLU* 5.6 0.2 - - - -
250A ARG* 4.1 7.0 - - - +
443A LEU* 1.3 76.9 - - - +
445A TYR* 1.3 65.7 + - - +
446A MET* 3.5 1.0 + - - +
447A ARG* 3.1 38.6 + - - +
448A ILE* 3.3 9.1 + - - +
219C ILE* 5.1 4.0 - - + -
220C PRO* 3.2 31.3 - - + +
223C SER* 5.9 0.3 - - - -
224C TYR* 2.6 43.1 + - + +
295D ILE* 4.9 11.0 - - + -
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Residues in contact with TYR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLY* 3.7 1.7 - - - -
247A SER* 3.9 16.4 - - - -
248A GLU* 3.5 39.1 + - + +
250A ARG* 4.0 0.4 - - - +
430A ASP* 3.6 2.9 + - - -
431A ILE* 2.7 54.6 + - + -
433A ILE* 4.1 9.2 - - + -
444A ASP* 1.3 73.1 - - - +
446A MET* 1.3 62.4 + - + +
448A ILE* 3.0 10.8 + - - +
449A ARG* 2.8 42.5 + - + +
224C TYR* 4.6 1.1 + - - +
294D GLY* 6.2 3.6 - - - -
28H ALA* 5.6 4.5 - - + -
29H VAL 5.4 1.1 - - - -
30H SER* 3.4 45.2 - - - -
31H PRO* 4.2 9.9 - - + -
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Residues in contact with MET 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP* 3.4 2.9 + - - +
445A TYR* 1.3 84.2 - - + +
447A ARG* 1.3 54.3 - - - +
449A ARG* 3.9 14.0 - - - +
450A SER* 2.7 42.1 + - - +
514A PCF 6.6 0.4 - - - -
223C SER* 5.1 10.3 - - - +
224C TYR* 3.6 21.6 + - + +
290D PHE* 4.0 28.9 - - + -
291D LYS* 4.0 29.8 - - + +
294D GLY* 6.0 1.8 - - - +
31H PRO* 3.8 33.7 - - + -
32H TYR* 4.2 12.1 - - + +
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.4 35.0 - - + +
444A ASP* 3.1 35.4 + - - +
445A TYR 3.1 0.6 + - - -
446A MET* 1.3 74.3 - - - +
448A ILE* 1.3 67.1 + - + +
450A SER* 3.7 7.3 + - - -
451A ASP* 3.7 19.9 + - - +
514A PCF 5.7 2.0 - - - -
4C ARG* 3.5 16.0 - - - +
18C ILE* 3.1 35.4 + - - +
19C ASP* 2.6 29.3 + - - -
220C PRO* 4.0 8.3 - - + +
222C HIS* 3.8 30.4 + - - +
223C SER* 5.8 2.5 - - - -
224C TYR* 5.7 0.2 - - + -
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Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.5 24.0 - - + -
341A ASP* 6.4 1.3 - - - -
344A ILE* 3.8 28.0 - - + -
348A LEU* 3.4 22.4 - - + +
431A ILE* 3.5 22.7 - - + -
433A ILE* 4.0 14.6 - - + -
442A LEU* 4.7 7.2 - - + -
443A LEU* 4.0 27.1 - - + +
444A ASP 3.3 15.9 - - - +
445A TYR 3.0 5.1 + - - +
447A ARG* 1.3 78.6 - - + +
449A ARG* 1.3 62.9 + - - +
451A ASP* 3.0 13.5 + - - +
452A MET* 3.9 1.2 + - - +
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Residues in contact with ARG 449 (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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428A ASP* 2.6 49.7 + - - +
429A GLN 3.2 23.4 + - - +
430A ASP* 2.5 47.1 + - - +
431A ILE* 3.9 12.9 - - + +
445A TYR* 2.8 36.1 + - + +
446A MET* 3.9 10.1 - - - +
448A ILE* 1.3 77.9 - - - +
450A SER* 1.3 61.2 + - - +
452A MET* 3.1 22.7 + - - +
453A SER* 5.5 0.3 + - - -
521A UMQ 5.7 0.7 + - - -
53E ARG* 3.6 7.5 - - - +
32H TYR* 3.0 42.6 + - + -
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Residues in contact with SER 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A MET* 2.7 29.3 + - - +
447A ARG* 3.9 9.6 - - - -
448A ILE 3.2 0.4 - - - -
449A ARG* 1.3 76.7 - - - +
451A ASP* 1.3 59.6 + - - +
452A MET 3.1 4.4 + - - -
453A SER* 3.6 19.9 + - - +
514A PCF 3.1 52.5 - - - -
521A UMQ 5.5 0.4 - - - -
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Residues in contact with ASP 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 5.0 1.2 - - - +
345A HIS* 3.1 33.9 + - - +
348A LEU* 3.8 25.1 - - + +
349A LYS* 3.2 27.4 + - - +
352A ASN* 3.2 19.2 + - - +
447A ARG 3.7 10.1 + - - +
448A ILE* 3.0 14.6 + - - +
450A SER* 1.3 76.3 - - - +
452A MET* 1.3 55.1 + - - +
453A SER 3.0 11.4 + - - -
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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
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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