Contacts of the helix formed by residues 510 - 528 (chain u) 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 510 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24t ASP* 3.9 8.5 - - - +
435u GLU* 4.4 2.0 - - - +
508u ASP* 3.1 19.6 - - - +
509u ALA* 1.3 77.8 - - - +
511u VAL* 1.3 67.2 + - + +
512u ASP* 3.4 8.8 + - - +
513u GLY* 2.7 34.8 + - - -
514u ALA* 3.4 14.6 + - - +
517u ARG* 5.4 1.0 + - - -
580u TYR 5.8 1.6 - - - +
581u LYS 3.4 22.2 - - - +
8w C 5.7 3.2 + - - +
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Residues in contact with VAL 511 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24t ASP* 3.8 27.4 - - - +
25t TYR* 3.4 17.3 - - + +
28t SER* 3.3 40.6 - - - +
29t VAL 5.7 0.2 - - - +
33t ARG* 3.7 21.8 - - - +
81t HIS* 5.8 2.9 - - + -
510u ASP* 1.3 78.1 - - + +
512u ASP* 1.3 65.4 + - - +
513u GLY 3.2 0.2 - - - -
514u ALA* 3.2 5.4 + - - +
515u HIS 3.1 20.4 + - - -
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Residues in contact with ASP 512 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25t TYR* 3.4 4.4 - - - -
33t ARG* 2.6 42.1 + - - -
81t HIS* 4.7 2.9 - - - -
435u GLU* 4.5 2.5 - - - +
460u LYS* 2.9 26.8 + - - -
510u ASP* 3.4 7.1 + - - +
511u VAL* 1.3 79.0 - - - +
513u GLY* 1.3 59.5 + - - +
515u HIS* 3.8 5.9 - - - +
516u ILE* 3.2 34.7 + - - +
7w A 3.8 1.6 - - - +
8w C 3.4 41.6 - - - +
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Residues in contact with GLY 513 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435u GLU* 3.4 21.2 + - - -
507u THR* 3.3 17.7 + - - +
508u ASP 3.6 12.1 - - - -
510u ASP* 2.7 16.2 + - - -
511u VAL 3.2 0.2 - - - -
512u ASP* 1.3 73.8 - - - +
514u ALA* 1.3 57.7 + - - +
516u ILE* 3.2 2.5 + - - -
517u ARG* 2.9 26.1 + - - +
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Residues in contact with ALA 514 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21t SER* 3.2 27.5 - - - +
24t ASP* 3.6 18.8 - - + +
510u ASP 3.4 7.2 + - - +
511u VAL 3.2 11.3 + - - +
513u GLY* 1.3 73.1 - - - +
515u HIS* 1.3 55.8 + - - +
517u ARG* 3.3 32.0 - - - +
518u THR* 3.0 31.5 + - - +
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Residues in contact with HIS 515 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22t PHE* 4.4 5.4 - + - -
25t TYR* 3.3 56.2 - + + +
460u LYS* 3.3 23.9 + - + +
511u VAL 3.1 5.7 + - - -
512u ASP 3.8 7.2 - - - +
513u GLY 3.2 0.4 - - - -
514u ALA* 1.3 76.2 - - - +
516u ILE* 1.3 55.2 + - - +
518u THR* 2.7 31.2 + - - -
519u LEU* 3.0 28.0 + - + +
2015v A 2.8 46.7 + - - -
2016v C 2.9 14.0 + - - -
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Residues in contact with ILE 516 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435u GLU* 3.5 35.7 - - + +
457u LEU* 4.8 5.6 - - + -
459u GLY* 4.1 22.2 - - - +
460u LYS* 4.0 26.2 - - + +
461u ILE* 4.7 15.0 - - + +
507u THR* 4.0 14.8 - - + -
512u ASP 3.2 19.3 + - - +
513u GLY 3.2 3.8 + - - +
515u HIS* 1.3 73.4 - - - +
517u ARG* 1.3 56.3 + - - +
519u LEU* 3.4 7.7 + - - +
520u LEU* 3.1 41.6 + - + +
8w C 4.8 5.2 - - + +
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Residues in contact with ARG 517 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17t GLU* 2.4 30.2 + - - +
21t SER* 2.9 19.9 + - - +
24t ASP* 5.3 0.8 + - - -
505u ILE* 4.1 20.8 - - + +
507u THR* 2.9 29.1 + - - +
508u ASP 4.4 6.1 + - - -
510u ASP 5.4 1.0 + - - -
513u GLY 2.9 10.4 + - - +
514u ALA* 3.3 33.5 - - - +
515u HIS 3.2 0.2 - - - -
516u ILE* 1.3 74.6 - - - +
518u THR* 1.3 57.6 + - - +
519u LEU 3.3 0.2 + - - -
520u LEU* 3.4 2.9 + - - +
521u LEU* 3.0 44.6 + - + +
539u ILE* 3.9 25.0 - - + +
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Residues in contact with THR 518 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18t MET* 3.4 30.5 - - + +
21t SER* 3.5 9.6 - - - -
22t PHE* 3.3 41.0 - - + +
514u ALA 3.0 17.9 + - - +
515u HIS* 2.7 26.3 + - - -
517u ARG* 1.3 75.4 - - - +
519u LEU* 1.3 52.5 + - - +
521u LEU* 4.9 0.4 - - - -
522u THR* 2.6 37.5 + - - -
622u MET* 3.7 15.1 - - - +
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Residues in contact with LEU 519 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460u LYS* 4.1 12.8 - - + -
461u ILE* 3.6 42.5 - - + +
462u LEU 4.6 3.5 - - - +
463u ASN* 3.7 37.0 - - + +
464u VAL* 5.2 1.4 + - - +
515u HIS* 3.0 53.4 + - + +
516u ILE* 3.7 9.2 - - - +
517u ARG 3.2 0.4 - - - -
518u THR* 1.3 73.7 + - - +
520u LEU* 1.3 64.7 + - - +
522u THR* 3.5 4.4 + - - -
523u PHE* 3.2 16.1 + - - +
622u MET* 3.7 16.2 - - + -
2015v A 4.1 5.8 - - - +
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Residues in contact with LEU 520 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433u LEU* 4.6 13.0 - - + +
457u LEU* 3.9 24.9 - - + -
461u ILE* 3.9 18.6 - - + -
481u MET* 3.6 32.1 - - + -
505u ILE* 4.0 35.4 - - + -
507u THR* 4.8 2.9 - - + -
516u ILE* 3.1 29.2 + - + +
517u ARG 3.8 3.8 - - - +
519u LEU* 1.3 74.0 - - - +
521u LEU* 1.3 54.6 + - - +
522u THR 3.2 0.2 - - - -
523u PHE* 3.0 5.8 + - - +
524u PHE* 2.9 43.4 + - + -
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Residues in contact with LEU 521 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14t ILE* 4.2 21.3 - - + +
17t GLU* 3.4 35.4 - - + -
18t MET* 3.4 31.0 - - + +
505u ILE* 3.9 21.8 - - + -
517u ARG* 3.0 25.4 + - + +
518u THR* 4.9 0.4 - - + -
520u LEU* 1.3 74.7 - - - +
522u THR* 1.3 56.5 + - - +
524u PHE* 3.5 6.3 + - + +
525u TYR* 2.9 33.1 + - - +
532u ILE* 5.6 0.4 - - + -
537u VAL* 4.3 15.0 - - + -
539u ILE* 4.5 1.6 - - + -
606u VAL* 4.4 8.7 - - + -
618u PHE* 3.7 6.6 - - + -
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Residues in contact with THR 522 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463u ASN* 4.2 4.3 - - - +
464u VAL* 3.9 12.1 - - + +
465u GLU* 3.9 34.1 - - + +
518u THR 2.6 23.7 + - - -
519u LEU* 3.6 8.1 - - - -
520u LEU 3.2 0.2 - - - -
521u LEU* 1.3 74.4 - - - +
523u PHE* 1.3 62.0 + - - +
525u TYR* 4.0 0.7 - - - +
526u ARG* 3.2 26.2 + - + +
618u PHE* 3.2 20.7 - - + -
622u MET* 3.2 26.2 - - + +
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Residues in contact with PHE 523 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461u ILE* 4.5 6.3 - - + -
464u VAL* 3.6 24.6 - - + +
472u ILE* 5.2 0.2 - - + -
478u ILE* 3.7 33.7 - - + -
481u MET* 3.6 30.7 - - + -
482u ILE* 4.0 25.4 - - + -
519u LEU 3.2 12.6 + - - +
520u LEU* 3.0 10.6 + - + +
522u THR* 1.3 72.8 - - - +
524u PHE* 1.3 82.5 + + - +
526u ARG 3.4 0.9 + - - -
527u PHE* 3.0 56.7 + + + +
528u MET* 4.1 17.3 - - + -
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Residues in contact with PHE 524 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433u LEU* 3.7 24.2 - - + -
481u MET* 4.6 5.2 - - - -
485u PHE* 3.4 26.5 - + - -
503u ILE* 3.8 14.4 - - + -
505u ILE* 3.8 32.1 - - + -
520u LEU* 2.9 28.5 + - + +
521u LEU* 3.8 6.7 - - + +
522u THR 3.5 0.2 - - - -
523u PHE* 1.3 90.2 - + - +
525u TYR* 1.3 57.0 - - - +
528u MET* 2.9 53.8 + - + +
531u LEU* 5.2 2.9 - - + -
532u ILE* 3.8 18.4 - - + -
537u VAL* 4.2 19.5 - - + -
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Residues in contact with TYR 525 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14t ILE* 4.3 9.9 - - + -
521u LEU 2.9 19.0 + - - +
522u THR 4.1 2.7 - - - +
524u PHE* 1.3 76.5 - - - +
526u ARG* 1.3 75.6 + - + +
529u ARG* 3.4 65.2 + - + +
532u ILE* 3.6 11.6 - - + +
608u LEU* 3.8 19.3 - - + -
611u ALA* 3.0 20.8 + - - -
614u ALA* 3.4 19.8 - - + +
615u ASP* 3.0 24.4 + - - -
618u PHE* 3.6 37.0 - + + -
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Residues in contact with ARG 526 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464u VAL* 4.4 5.6 - - + -
465u GLU* 2.8 41.4 + - - +
490u GLY* 5.6 2.6 - - - -
522u THR* 3.2 21.0 + - + +
525u TYR* 1.3 93.3 - - + +
527u PHE* 1.3 81.6 + - + +
529u ARG* 3.9 8.4 - - - +
615u ASP* 3.1 49.8 + - - +
618u PHE* 3.8 10.5 - - + +
619u GLU* 4.1 3.8 + - - +
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Residues in contact with PHE 527 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464u VAL* 4.1 18.8 - - + -
469u LEU* 3.9 25.1 - - + -
472u ILE* 3.7 32.1 - - + -
482u ILE* 5.9 0.2 - - + -
489u ILE* 3.6 36.0 - - + -
490u GLY* 3.1 29.2 + - - +
493u PHE* 4.6 2.1 - - - +
523u PHE* 3.0 39.1 + + + +
526u ARG* 1.3 100.7 - - + +
528u MET* 1.3 63.2 + - + +
529u ARG 3.9 1.6 - - - -
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Residues in contact with MET 528 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482u ILE* 3.9 20.4 - - + +
485u PHE* 3.6 29.4 - - + -
487u THR* 3.9 12.6 - - - +
488u GLY 3.9 2.2 - - - +
489u ILE* 3.8 21.8 - - + -
493u PHE* 3.9 16.2 - - + -
523u PHE* 4.1 9.6 - - + -
524u PHE* 2.9 29.1 + - + +
527u PHE* 1.3 86.0 - - + +
529u ARG* 1.3 63.9 + - - +
530u PRO* 3.3 9.0 - - - -
531u LEU* 3.1 44.6 + - + +
532u ILE* 3.8 2.4 + - - +
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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