Contacts of the helix formed by residues 461 - 481 (chain L) in PDB entry 6QX2
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 461 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457L THR* 3.2 7.7 + - + +
458L ILE 3.3 6.3 - - - +
459L LEU 3.5 0.4 - - - -
460L ALA* 1.3 77.9 - - + +
462L GLU* 1.3 57.7 + - - +
463L GLU* 3.2 20.3 + - - +
464L VAL* 2.9 49.6 + - + +
465L LEU 3.2 8.3 + - - -
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Residues in contact with GLU 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458L ILE 4.9 0.7 - - - -
459L LEU 5.2 2.4 + - - +
460L ALA 4.1 2.6 + - - -
461L ASP* 1.3 73.0 + - - +
463L GLU* 1.3 56.6 + - - +
465L LEU* 3.4 18.6 + - + +
466L LEU* 3.0 30.1 + - - +
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Residues in contact with GLU 463 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461L ASP* 3.1 17.2 + - - +
462L GLU* 1.3 74.5 - - - +
464L VAL* 1.3 65.4 + - + +
466L LEU* 3.6 15.5 + - - +
467L GLN* 3.1 24.6 + - - +
470L ARG* 3.3 27.9 + - - -
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Residues in contact with VAL 464 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457L THR* 4.1 19.7 - - + +
458L ILE* 3.7 31.9 - - + +
461L ASP* 2.9 34.8 + - + +
463L GLU* 1.3 76.7 - - - +
465L LEU* 1.3 56.1 + - - +
467L GLN* 3.3 8.3 + - - +
468L LEU* 3.1 24.8 + - - +
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Residues in contact with LEU 465 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360L LYS* 4.3 31.2 - - + +
363L VAL* 4.6 7.7 - - + +
364L ARG* 3.7 39.7 - - + -
458L ILE* 3.7 37.2 - - + +
459L LEU* 5.3 3.6 - - + -
461L ASP 3.2 3.3 + - - +
462L GLU* 3.6 21.1 - - + +
464L VAL* 1.3 76.6 - - - +
466L LEU* 1.3 70.8 + - + +
468L LEU* 3.0 16.8 + - - +
469L VAL* 3.0 15.9 + - + +
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Residues in contact with LEU 466 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L SER* 3.5 23.8 - - - +
356L LEU* 4.6 10.1 - - + -
360L LYS* 3.9 31.2 - - + -
462L GLU 3.0 17.2 + - - +
463L GLU* 3.8 17.3 - - - +
465L LEU* 1.3 81.5 - - + +
467L GLN* 1.3 57.0 + - - +
469L VAL* 3.2 8.9 + - + +
470L ARG* 3.0 58.4 + - - +
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Residues in contact with GLN 467 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463L GLU* 3.1 21.9 + - - +
464L VAL* 3.4 8.3 - - - +
465L LEU 3.2 0.2 - - - -
466L LEU* 1.3 73.1 - - - +
468L LEU* 1.3 56.4 + - - +
470L ARG* 3.1 34.9 + - - +
471L ASP* 2.7 76.1 + - - +
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Residues in contact with LEU 468 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363L VAL* 3.8 16.2 - - + -
366L ARG* 3.7 18.6 - - - +
367L THR* 4.6 1.8 - - - +
458L ILE* 3.8 34.1 - - + -
464L VAL* 3.1 11.7 + - + +
465L LEU* 3.0 14.7 + - - +
467L GLN* 1.3 72.8 - - - +
469L VAL* 1.3 62.4 + - - +
471L ASP* 3.3 9.5 + - + +
472L GLU* 3.0 52.1 + - + +
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Residues in contact with VAL 469 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163L ARG* 5.1 3.2 + - - +
356L LEU* 4.1 16.2 - - + -
359L GLN* 4.0 26.7 - - + +
360L LYS* 4.2 13.0 - - + -
363L VAL* 3.9 32.1 - - + -
465L LEU* 3.0 21.2 + - + +
466L LEU* 3.2 11.6 + - + +
468L LEU* 1.3 76.0 - - - +
470L ARG* 1.3 64.4 + - + +
472L GLU* 3.3 3.0 + - - +
473L LEU* 3.0 42.4 + - + +
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Residues in contact with ARG 470 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196L LEU* 3.7 21.7 - - + +
199L SER* 2.9 51.2 + - - +
200L LYS* 3.7 24.7 - - - +
463L GLU* 3.3 22.2 + - - -
466L LEU* 3.0 30.0 + - - +
467L GLN* 3.1 50.6 + - - +
469L VAL* 1.3 77.1 - - + +
471L ASP* 1.3 58.1 + - - +
473L LEU* 3.5 4.6 + - - +
474L THR* 2.9 34.6 + - - +
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Residues in contact with ASP 471 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467L GLN* 2.7 54.0 + - - +
468L LEU* 3.7 11.8 + - + +
470L ARG* 1.3 76.5 - - - +
472L GLU* 1.3 58.3 + - + +
474L THR* 3.3 8.7 + - - -
475L GLU* 3.1 27.1 + - - +
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Residues in contact with GLU 472 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163L ARG* 2.8 47.6 + - - +
363L VAL* 4.1 2.3 - - - +
366L ARG* 2.9 32.7 + - - -
468L LEU* 3.0 37.1 + - + +
469L VAL 3.9 1.6 - - - +
471L ASP* 1.3 72.4 - - + +
473L LEU* 1.3 64.5 + - - +
475L GLU* 3.4 10.1 + - - +
476L ILE* 3.2 30.6 + - + +
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Residues in contact with LEU 473 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163L ARG* 3.8 23.7 - - - +
165L PRO* 4.5 2.2 - - + -
192L ILE* 3.6 37.5 - - + +
195L VAL* 3.7 30.3 - - + -
196L LEU* 4.6 10.1 - - + -
355L TYR* 4.1 20.4 - - + +
356L LEU* 5.0 1.1 - - + -
359L GLN* 5.1 4.7 - - + +
469L VAL* 3.0 37.6 + - + +
470L ARG* 3.6 4.7 - - - +
472L GLU* 1.3 75.4 - - - +
474L THR* 1.3 51.9 + - - +
476L ILE* 3.2 8.7 + - - +
477L ARG* 2.9 32.7 + - - +
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Residues in contact with THR 474 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L ILE* 4.8 1.3 - - - -
196L LEU* 3.6 19.9 - - - +
470L ARG* 2.9 21.4 + - - +
471L ASP* 3.5 9.2 - - - +
472L GLU 3.3 0.2 - - - -
473L LEU* 1.3 73.6 - - - +
475L GLU* 1.3 58.7 + - - +
477L ARG* 3.3 30.7 + - - +
478L ASP* 3.0 38.4 + - - +
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Residues in contact with GLU 475 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471L ASP 3.1 13.4 + - - +
472L GLU* 3.5 12.6 - - - +
473L LEU 3.3 0.2 - - - -
474L THR* 1.3 76.2 - - - +
476L ILE* 1.3 57.7 + - + +
478L ASP* 3.4 7.8 + - - +
479L ARG* 3.1 35.6 + - - +
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Residues in contact with ILE 476 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L ILE* 6.0 0.2 - - + -
134L GLU* 3.6 34.5 - - + +
163L ARG* 3.2 39.0 - - + +
164L PHE* 4.0 17.7 - - + -
188L LEU* 4.5 4.9 - - + -
192L ILE* 3.9 17.3 - - + -
472L GLU* 3.2 22.6 + - + +
473L LEU* 3.5 6.5 - - - +
475L GLU* 1.3 71.9 - - + +
477L ARG* 1.3 61.3 + - - +
479L ARG* 3.3 8.5 + - - +
480L PHE* 2.9 44.7 + - + +
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Residues in contact with ARG 477 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L LEU* 5.3 0.7 - - - -
189L THR* 3.9 36.5 + - + +
192L ILE* 3.7 24.9 - - + -
193L ASN* 2.7 37.3 + - - -
196L LEU* 3.7 18.8 - - - +
473L LEU 2.9 14.2 + - - +
474L THR* 3.3 27.3 + - - +
476L ILE* 1.3 75.6 - - - +
478L ASP* 1.3 80.6 + - - +
481L GLY* 2.8 31.4 + - - +
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Residues in contact with ASP 478 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474L THR* 3.0 30.9 + - - +
475L GLU* 3.8 6.7 - - - +
476L ILE 3.2 0.4 - - - -
477L ARG* 1.3 101.7 + - - +
479L ARG* 1.3 59.4 + - - +
481L GLY 5.0 2.4 + - - +
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Residues in contact with ARG 479 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L LYS* 5.3 1.6 + - - +
134L GLU* 3.3 28.9 + - - -
475L GLU* 3.1 18.8 + - - +
476L ILE* 4.0 14.8 - - - +
478L ASP* 1.3 78.8 - - - +
480L PHE* 1.3 95.7 + - + +
481L GLY 4.9 1.2 - - - +
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Residues in contact with PHE 480 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L TYR* 4.1 17.0 - - - -
130L LYS* 3.8 20.6 - - + -
131L ILE* 3.7 48.2 - - + -
134L GLU* 3.7 17.9 - - + -
188L LEU* 3.8 17.5 - - + -
476L ILE* 2.9 25.7 + - + +
479L ARG* 1.3 119.1 - - + +
481L GLY* 1.3 71.1 + - - +
482L ASP* 3.6 3.5 + - - +
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Residues in contact with GLY 481 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L LEU* 4.1 6.1 - - - +
189L THR* 3.1 24.2 - - - -
476L ILE 3.8 0.4 + - - -
477L ARG* 2.8 24.1 + - - +
478L ASP 5.1 1.9 - - - +
479L ARG 4.9 1.7 - - - +
480L PHE* 1.3 81.8 + - - +
482L ASP* 1.3 59.0 + - - +
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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
------------------------------------------------------------
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