Contacts of the helix formed by residues 512 - 527 (chain B) in PDB entry 1Q6X
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 ILE 512 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B THR* 3.9 28.0 - - + +
37B THR* 3.7 31.9 - - + -
38B TYR* 3.9 32.3 - - + +
41B CYS* 4.5 3.1 - - + -
463B ARG* 4.1 19.3 - - - +
502B TYR* 3.8 13.6 + - - +
505B MET* 5.3 1.1 - - + -
510B MET 4.9 2.0 - - - +
511B ALA* 1.3 84.5 - - - +
513B ASP* 1.3 77.6 + - - +
514B ASN 3.5 1.3 - - - -
515B HIS* 3.1 5.2 + - - +
516B LEU* 2.9 34.7 + - + +
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Residues in contact with ASP 513 (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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446B TYR* 5.0 1.0 - - - -
460B ASP* 3.3 15.3 + - - +
461B ASN* 3.3 29.8 + - + +
463B ARG* 2.9 42.9 + - - +
502B TYR* 4.8 0.7 + - - -
511B ALA* 4.0 0.6 - - - +
512B ILE* 1.3 81.7 - - - +
514B ASN* 1.3 65.3 + - - +
516B LEU* 3.3 6.0 + - - +
517B LEU* 2.9 24.2 + - - +
543B ASN* 4.4 3.6 - - - +
545B PHE* 3.8 9.4 - - - -
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Residues in contact with ASN 514 (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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26B LEU* 5.0 3.5 - - + +
85B TRP* 3.5 20.0 - - + -
86B VAL* 3.9 23.4 - - + +
90B TRP* 3.6 24.9 - - - -
451B ILE* 4.0 13.3 - - - +
459B VAL 3.2 16.5 + - - +
460B ASP* 3.1 35.2 + - - +
513B ASP* 1.3 79.1 - - - +
515B HIS* 1.3 63.0 + - - +
517B LEU* 3.3 9.3 + - - +
518B ALA 3.1 17.5 + - - -
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Residues in contact with HIS 515 (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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28B VAL* 4.1 1.0 - - - +
29B PRO* 3.0 49.5 + - + +
30B PRO 4.0 3.6 - - - -
31B LEU* 4.2 4.0 - - + -
34B THR* 2.6 37.1 + - + +
72B GLN* 2.7 27.8 + - - -
75B LEU* 3.5 19.8 - - + +
85B TRP* 3.9 9.5 - + + -
511B ALA 4.4 2.6 + - - +
512B ILE 3.1 11.0 + - - +
514B ASN* 1.3 77.0 - - - +
516B LEU* 1.3 63.4 + - - +
518B ALA* 3.2 3.8 + - - +
519B LEU* 3.1 30.8 + - + +
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Residues in contact with LEU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 3.8 20.4 - - + -
35B LEU* 4.5 5.8 - - + -
38B TYR* 3.9 31.2 - - + -
61B PHE* 5.7 0.2 - - + -
463B ARG* 6.4 0.2 - - - +
512B ILE* 2.9 32.9 + - + +
513B ASP* 3.9 4.9 - - - +
515B HIS* 1.3 76.3 - - - +
517B LEU* 1.3 63.8 + - - +
519B LEU* 3.4 16.5 + - + +
520B ARG* 3.0 25.3 + - - +
533B MET* 4.3 21.1 - - + -
534B PHE* 3.9 8.2 - - + -
539B TYR* 4.3 24.7 - - + +
542B SER* 6.0 0.4 - - - +
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Residues in contact with LEU 517 (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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86B VAL* 4.0 13.0 - - + -
89B TYR* 4.0 8.5 - - + +
90B TRP* 3.9 37.9 - - + +
93B ASP* 3.7 22.0 - - + +
513B ASP 2.9 15.2 + - - +
514B ASN* 3.4 13.0 - - - +
515B HIS 3.2 0.2 - - - -
516B LEU* 1.3 78.5 - - - +
518B ALA* 1.3 57.0 + - - +
520B ARG* 3.2 38.2 + - - +
521B GLU* 3.0 34.1 + - + +
539B TYR* 4.7 4.9 + - - +
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Residues in contact with ALA 518 (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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75B LEU* 3.8 21.1 - - + -
85B TRP* 3.6 31.6 - - + -
86B VAL* 5.3 0.4 - - + -
89B TYR* 3.8 20.6 - - + -
514B ASN 3.1 5.8 + - - +
515B HIS 3.2 4.9 + - - +
517B LEU* 1.3 75.7 - - - +
519B LEU* 1.3 60.8 + - - +
521B GLU* 3.3 1.0 + - - +
522B LEU* 2.8 36.3 + - - +
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.9 23.3 - - + -
34B THR* 5.6 0.2 - - + -
35B LEU* 5.5 0.4 - - + -
61B PHE* 4.4 13.5 - - + -
68B GLY 4.7 2.0 - - - +
71B LEU* 3.5 35.9 - - + +
72B GLN* 4.0 24.2 - - + +
75B LEU* 4.2 9.6 - - + -
515B HIS* 3.1 27.1 + - + +
516B LEU* 3.8 21.5 - - + +
518B ALA* 1.3 76.3 - - - +
520B ARG* 1.3 56.5 + - - +
522B LEU* 3.3 4.1 + - + +
523B ALA* 2.9 30.3 + - - +
534B PHE* 4.0 11.0 - - + -
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Residues in contact with ARG 520 (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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93B ASP* 2.8 30.5 + - - +
516B LEU 3.0 18.2 + - - +
517B LEU* 3.2 22.7 - - - +
519B LEU* 1.3 77.3 - - - +
521B GLU* 1.3 82.7 + - - +
523B ALA* 3.2 4.2 + - - +
524B ARG* 3.1 25.9 + - + +
531B PRO* 5.8 0.2 - - - +
534B PHE* 3.3 36.4 - - + -
539B TYR* 3.2 36.9 + - - +
543B ASN* 4.6 6.1 - - - +
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Residues in contact with GLU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.7 47.9 + - + +
93B ASP* 6.3 0.7 - - - -
517B LEU* 3.0 25.0 + - + +
518B ALA 4.0 0.7 - - - +
520B ARG* 1.3 108.6 + - - +
522B LEU* 1.3 66.0 + - - +
524B ARG* 3.2 40.2 + - - +
525B ASP* 3.2 21.8 + - - +
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Residues in contact with LEU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.9 19.1 - - + +
74B LYS* 4.3 15.9 - - + +
75B LEU* 3.8 45.5 - - + +
78B ARG* 4.5 10.3 - - + +
89B TYR* 3.5 21.1 - - + +
518B ALA 2.8 23.1 + - - +
519B LEU* 3.7 6.7 - - - +
521B GLU* 1.3 77.2 - - - +
523B ALA* 1.3 63.1 + - - +
525B ASP* 3.4 5.0 + - + -
526B LEU* 3.2 37.5 + - + +
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Residues in contact with ALA 523 (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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71B LEU* 3.8 19.9 - - + +
519B LEU 2.9 17.1 + - - +
520B ARG* 3.5 7.9 - - - +
521B GLU 3.2 0.2 - - - -
522B LEU* 1.3 78.1 - - - +
524B ARG* 1.3 59.5 + - - +
527B CYS* 2.6 44.0 + - - +
531B PRO* 3.7 32.3 - - + -
534B PHE* 4.7 1.1 - - + -
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Residues in contact with ARG 524 (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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520B ARG* 3.1 14.0 + - + +
521B GLU* 3.2 37.9 + - - +
522B LEU 3.3 0.4 - - - -
523B ALA* 1.3 76.5 - - - +
525B ASP* 1.3 62.5 + - - +
526B LEU 3.6 0.3 + - - -
527B CYS 4.0 10.6 - - - +
530B PRO* 6.5 0.7 - - - -
531B PRO* 6.0 1.8 - - - -
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Residues in contact with ASP 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 6.0 0.9 - - - +
521B GLU 3.2 13.1 + - - +
522B LEU* 3.8 8.1 - - + +
523B ALA 3.1 0.8 - - - -
524B ARG* 1.3 84.9 + - - +
526B LEU* 1.3 71.8 + - + +
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Residues in contact with LEU 526 (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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70B THR* 6.5 0.7 - - + -
71B LEU* 4.7 9.2 - - + -
74B LYS* 4.1 37.2 - - + -
522B LEU* 3.2 25.5 + - + +
523B ALA* 3.1 3.2 + - - -
525B ASP* 1.3 97.8 - - + +
527B CYS* 1.3 65.3 + - - +
528B LYS* 4.0 5.8 + - - +
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Residues in contact with CYS 527 (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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67B LEU* 3.8 29.2 - - - -
71B LEU* 5.0 1.8 - - - -
523B ALA* 2.6 39.8 + - - +
524B ARG* 4.0 9.7 - - - +
526B LEU* 1.3 77.9 - - - +
528B LYS* 1.3 66.2 + - - +
529B GLU* 3.3 20.3 + - - +
531B PRO* 4.4 7.0 - - + -
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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
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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