Contacts of the helix formed by residues 507 - 526 (chain A) in PDB entry 4DGX
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 507 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLY* 5.4 8.3 - - - +
58A ASN* 3.8 18.2 - - + +
59A THR 4.8 0.7 - - - -
60A GLY* 3.6 30.0 - - - +
251A PHE* 3.7 7.0 - - - -
505A VAL* 3.8 1.6 - - - +
506A GLN* 1.3 81.2 - - - +
508A GLU* 1.3 59.3 + - - +
509A ALA* 3.4 12.6 - - - +
510A GLN* 2.8 36.2 + - - +
511A TYR* 2.8 25.5 + - - +
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Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE 4.2 10.3 - - - +
248A TRP* 3.6 31.1 - - - +
251A PHE* 3.5 45.8 - - + +
252A GLU* 4.9 0.7 - - - +
507A THR* 1.3 70.1 - - - +
509A ALA* 1.3 66.7 + - - +
511A TYR* 3.1 2.9 + - + -
512A ARG* 2.5 63.8 + - + +
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Residues in contact with ALA 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLY* 5.4 5.8 - - - -
428A VAL* 4.1 22.8 - - + +
507A THR* 3.4 12.0 - - - +
508A GLU* 1.3 79.2 - - - +
510A GLN* 1.3 56.4 + - - +
512A ARG* 3.5 7.8 + - - +
513A PHE* 2.9 28.1 + - - +
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Residues in contact with GLN 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY* 3.2 27.9 + - - -
423A TRP* 4.6 5.5 - - + +
428A VAL* 3.8 21.8 - - + -
464A GLY 3.4 14.3 + - - -
465A ARG* 3.6 11.7 - - - +
468A THR* 3.3 22.8 + - - +
505A VAL* 4.2 3.6 - - + -
506A GLN* 2.7 34.9 + - - -
507A THR* 2.8 28.6 + - - +
509A ALA* 1.3 71.1 - - - +
511A TYR* 1.3 63.7 - - - +
513A PHE* 3.2 5.2 + - - +
514A ILE* 2.9 28.2 + - - +
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Residues in contact with TYR 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE* 4.0 18.8 - + - -
250A GLU* 2.5 34.9 + - + +
251A PHE* 3.6 51.6 - + + -
254A LEU* 4.1 13.0 - - + -
490A VAL* 3.9 8.3 - - + -
491A PRO* 3.0 21.5 - - + +
494A ILE* 3.5 31.0 - - + -
505A VAL* 4.3 3.0 - - + +
507A THR 2.8 10.5 + - - +
508A GLU* 3.2 9.6 - - + +
510A GLN* 1.3 69.7 - - - +
512A ARG* 1.3 58.5 + - + +
514A ILE* 2.8 31.9 + - - +
515A TYR* 3.2 24.0 + + - -
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Residues in contact with ARG 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU 4.3 5.3 + - - -
234A SER* 4.8 7.1 + - - +
247A PHE* 3.4 63.6 - - + +
248A TRP* 4.8 3.6 - - - +
508A GLU* 2.5 58.6 + - + +
509A ALA* 3.7 5.8 - - - +
511A TYR* 1.3 72.6 - - - +
513A PHE* 1.3 58.0 + - - +
515A TYR* 3.1 4.3 + - - +
516A MET* 2.8 29.8 + - - +
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Residues in contact with PHE 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A TRP* 4.2 13.7 - + - -
428A VAL* 4.0 17.0 - - + -
429A PRO* 3.4 38.6 - - + -
432A PRO* 4.0 32.1 - - + -
435A VAL* 3.7 29.4 - - + -
468A THR* 4.2 11.9 - - + -
472A ILE* 3.8 25.6 - - + -
509A ALA 2.9 15.4 + - - +
510A GLN* 3.2 10.1 + - - +
512A ARG* 1.3 74.5 - - - +
514A ILE* 1.3 53.0 + - - +
516A MET* 3.2 14.9 + - - +
517A ALA* 2.8 35.6 + - + +
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Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A THR* 4.2 12.1 - - + +
471A VAL* 4.0 10.1 - - + -
472A ILE* 3.8 31.1 - - + +
475A LEU* 3.8 28.9 - - + -
490A VAL* 4.2 11.4 - - + -
494A ILE* 4.0 15.9 - - + -
505A VAL* 4.0 33.0 - - + -
510A GLN 2.9 18.9 + - - +
511A TYR* 2.8 15.1 + - - +
513A PHE* 1.3 67.7 - - - +
515A TYR* 1.3 64.2 + - - +
517A ALA* 3.2 2.4 + - - +
518A VAL* 2.9 24.4 + - + +
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Residues in contact with TYR 515 (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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219A THR 4.6 6.9 + - - -
221A ILE* 4.6 18.5 - - + +
226A ILE* 4.0 18.3 - - + +
229A ARG* 4.7 6.9 + - + +
230A VAL* 4.6 11.4 - - + -
233A LEU* 4.2 11.6 - - + +
247A PHE* 3.2 33.9 - + + -
250A GLU* 2.6 35.1 + - - -
490A VAL* 3.7 34.8 + - + +
491A PRO* 4.0 4.5 - - - +
511A TYR* 3.2 27.9 + + - -
512A ARG 3.1 8.0 + - - +
514A ILE* 1.3 77.9 - - - +
516A MET* 1.3 65.9 + - - +
518A VAL* 3.0 4.6 + - - +
519A GLN* 2.9 26.3 + - - +
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Residues in contact with MET 516 (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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230A VAL* 5.7 1.1 - - - +
429A PRO 4.8 0.7 - - - +
430A SER* 2.8 32.5 - - - +
431A ASP* 3.8 3.1 - - + +
432A PRO* 3.4 28.5 - - + -
512A ARG 2.8 16.9 + - - +
513A PHE* 3.5 22.2 - - - +
515A TYR* 1.3 71.5 - - - +
517A ALA* 1.3 58.5 + - - +
519A GLN* 3.5 12.6 - - - +
520A HIS* 2.9 31.2 + - + +
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Residues in contact with ALA 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A PRO* 3.6 26.7 - - + +
435A VAL* 5.6 1.1 - - + -
436A LEU* 3.6 18.3 - - + +
472A ILE* 4.0 23.6 - - + -
476A ILE* 5.0 0.4 - - - -
513A PHE* 2.8 21.6 + - + +
514A ILE 3.8 3.4 - - - +
515A TYR 3.1 0.2 - - - -
516A MET* 1.3 73.3 - - - +
518A VAL* 1.3 61.0 + - - +
520A HIS 3.6 0.2 + - - -
521A TYR* 3.0 27.0 + - - +
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Residues in contact with VAL 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 3.5 20.9 - - + -
472A ILE* 5.3 4.0 - - + +
475A LEU* 3.9 36.1 - - + -
476A ILE* 4.5 10.1 - - + -
479A ILE* 3.7 26.0 - - + -
488A ILE* 3.9 11.9 - - + -
490A VAL* 5.5 2.2 - - + -
514A ILE* 2.9 20.9 + - + +
515A TYR* 4.7 1.1 - - - -
517A ALA* 1.3 71.8 - - - +
519A GLN* 1.3 68.9 + - - +
521A TYR* 2.8 16.7 + - - +
522A ILE* 2.9 15.9 + - + +
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Residues in contact with GLN 519 (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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226A ILE* 3.4 29.1 - - + +
227A GLU* 4.3 10.3 + - - +
230A VAL* 2.9 39.7 - - + +
515A TYR 2.9 16.2 + - - +
516A MET* 3.5 11.5 + - - +
518A VAL* 1.3 75.3 - - - +
520A HIS* 1.3 60.1 + - - +
522A ILE* 2.8 22.2 + - - +
523A GLU* 3.0 43.7 + - + +
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Residues in contact with HIS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ASP* 4.1 11.2 + - - -
432A PRO* 3.5 30.7 - - + -
433A GLY* 4.2 15.7 - - - -
436A LEU* 3.3 18.7 - - + +
516A MET* 2.9 22.6 + - + +
517A ALA 3.8 3.1 - - - +
519A GLN* 1.3 76.7 - - - +
521A TYR* 1.3 56.1 + - - +
523A GLU* 3.7 9.4 + - - +
524A THR* 3.1 32.4 + - - +
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Residues in contact with TYR 521 (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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436A LEU* 4.3 13.9 - - + -
440A GLU* 3.9 20.1 + - - -
476A ILE* 3.4 49.0 - - + +
479A ILE* 3.5 35.0 - - + -
480A ARG* 3.5 31.0 + - - +
517A ALA 3.0 14.5 + - - +
518A VAL 2.8 11.3 + - - +
520A HIS* 1.3 74.2 + - - +
522A ILE* 1.3 62.2 + - + +
524A THR* 2.8 31.6 - - + +
525A LEU* 3.3 31.5 + - + +
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Residues in contact with ILE 522 (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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223A ALA* 4.0 18.2 - - + +
224A ALA* 4.8 3.8 - - - +
226A ILE* 3.7 23.6 - - + -
479A ILE* 3.7 43.5 - - + -
484A VAL* 3.7 21.3 - - + -
518A VAL* 2.9 18.9 + - + +
519A GLN 2.8 11.4 + - - +
521A TYR* 1.3 68.4 - - - +
523A GLU* 1.3 55.3 + - + +
524A THR 3.0 3.8 - - - -
525A LEU* 2.6 29.1 + - + +
526A GLN* 2.9 39.3 + - - +
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Residues in contact with GLU 523 (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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226A ILE* 6.0 0.9 - - + -
227A GLU* 3.2 31.7 - - + +
519A GLN* 3.0 44.8 + - + +
520A HIS* 3.9 9.1 - - - +
522A ILE* 1.3 75.1 - - + +
524A THR* 1.3 53.8 + - - +
526A GLN* 3.7 25.6 - - - +
527A ARG* 2.7 53.3 + - - +
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Residues in contact with THR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 5.3 1.6 - - + -
520A HIS* 3.1 29.2 + - + +
521A TYR* 2.8 42.4 - - + +
522A ILE 2.8 0.2 + - - -
523A GLU* 1.3 76.4 - - - +
525A LEU* 1.3 64.7 + - + +
527A ARG* 4.0 6.0 - - - +
528A ARG 3.4 15.9 + - - -
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Residues in contact with LEU 525 (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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479A ILE* 4.0 31.2 - - + +
480A ARG* 5.3 2.2 - - - -
483A GLY* 5.7 0.7 - - - -
484A VAL* 5.0 18.4 - - + +
521A TYR* 3.3 40.6 + - + +
522A ILE* 2.6 18.0 + - - +
524A THR* 1.3 71.1 - - + +
526A GLN* 1.3 56.9 + - + +
527A ARG 3.0 9.9 + - - -
528A ARG 3.5 8.0 + - - -
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Residues in contact with GLN 526 (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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224A ALA* 5.0 6.0 + - - +
227A GLU* 5.9 1.0 + - - -
484A VAL* 4.1 16.1 - - + +
522A ILE* 2.9 40.1 + - + +
523A GLU* 3.7 25.3 - - - +
525A LEU* 1.3 75.0 - - + +
527A ARG* 1.3 62.7 + - + +
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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