Contacts of the helix formed by residues 480 - 497 (chain A) in PDB entry 2D2O
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 ASN 480 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A GLU* 3.2 35.3 + - - +
437A ARG* 4.2 1.0 + - - -
458A ILE* 2.9 29.9 + - - +
459A GLY* 4.1 7.2 - - - +
478A GLU 4.1 0.4 + - - -
479A GLN* 1.3 70.9 - - - +
481A ARG* 1.3 60.5 + - - +
482A GLY* 3.2 6.4 + - - -
483A LEU* 3.0 28.8 + - + +
484A PHE* 3.2 17.9 + - - +
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Residues in contact with ARG 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 4.3 14.6 - - - -
184A GLU* 4.1 10.1 + - - -
458A ILE* 4.8 0.8 - - - +
476A GLU* 3.8 34.7 + - + +
477A LYS* 5.8 0.4 - - - +
479A GLN* 2.7 54.4 + - - +
480A ASN* 1.3 70.0 - - - +
482A GLY* 1.3 65.6 + - - +
484A PHE* 3.5 38.8 - - - +
485A GLU* 3.0 34.7 + - + +
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Residues in contact with GLY 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 3.4 15.1 + - - -
480A ASN* 3.2 7.2 + - - -
481A ARG* 1.3 77.7 - - - +
483A LEU* 1.3 61.7 + - - +
485A GLU* 3.4 7.1 + - - +
486A PHE* 3.1 21.8 + - - +
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLU* 4.3 8.5 - - + +
436A PHE* 3.7 21.5 - - + -
437A ARG* 3.4 15.4 - - + +
440A VAL* 5.4 0.7 - - + -
456A ASP 3.1 28.3 - - - +
457A GLU 3.6 8.3 - - - +
459A GLY* 3.6 16.2 - - - +
480A ASN* 3.0 28.7 + - - +
482A GLY* 1.3 73.6 - - - +
484A PHE* 1.3 59.9 + - - +
486A PHE* 2.8 21.8 + - + +
487A TYR* 2.8 46.1 + - + -
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 3.3 48.5 - + - -
184A GLU* 3.2 31.6 - - - -
185A LEU* 3.9 28.5 - - + -
457A GLU* 3.2 22.3 + - + +
458A ILE* 4.0 7.6 - - + -
480A ASN 3.2 8.6 + - - +
481A ARG* 3.5 34.1 - - - +
483A LEU* 1.3 79.9 - - - +
485A GLU* 1.3 62.5 + - - +
487A TYR* 3.3 5.5 + - - +
488A LYS* 3.0 48.8 + - + +
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Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLU* 4.3 1.0 - - - +
481A ARG* 3.0 27.4 + - + +
482A GLY* 3.8 6.1 - - - +
483A LEU 3.2 0.2 - - - -
484A PHE* 1.3 81.4 - - + +
486A PHE* 1.3 64.8 + - - +
488A LYS* 3.0 39.6 + - - +
489A GLU* 3.1 23.0 + - - +
492A ARG* 5.1 4.5 + - - -
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Residues in contact with PHE 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 3.4 69.8 - - + +
440A VAL* 4.5 5.8 - - + -
441A LEU* 4.2 17.9 - - + -
482A GLY 3.1 12.9 + - - +
483A LEU* 2.8 18.8 + - + +
485A GLU* 1.3 74.2 - - - +
487A TYR* 1.3 66.5 + - - +
489A GLU* 3.2 14.8 + - + +
490A LEU* 3.1 54.7 + - + +
557A LEU* 5.2 8.3 - - + -
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Residues in contact with TYR 487 (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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185A LEU* 3.8 11.9 - - + -
417A LEU* 4.5 5.7 - - - +
436A PHE* 3.6 15.3 - + - -
440A VAL* 3.5 37.9 - - + +
443A GLN* 4.8 3.7 + - - -
444A MET* 5.3 3.4 - - - -
452A ILE* 4.0 40.0 - - + +
456A ASP* 3.9 13.3 - - - +
457A GLU* 3.5 30.7 - - + -
483A LEU* 2.8 40.5 + - + -
484A PHE* 3.5 9.6 - - - +
486A PHE* 1.3 76.5 - - - +
488A LYS* 1.3 56.7 + - - +
490A LEU* 3.2 8.6 + - - +
491A ILE* 2.9 41.2 + - + +
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Residues in contact with LYS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLU* 2.9 48.8 + - - +
185A LEU* 4.0 20.8 - - + +
484A PHE* 3.0 40.1 + - + +
485A GLU* 3.0 36.1 + - - +
487A TYR* 1.3 77.3 - - - +
489A GLU* 1.3 57.4 + - - +
491A ILE* 3.3 1.9 + - - +
492A ARG* 2.9 52.5 + - + +
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Residues in contact with GLU 489 (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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485A GLU 3.1 13.1 + - - +
486A PHE* 3.2 14.4 + - + +
488A LYS* 1.3 76.5 - - - +
490A LEU* 1.3 58.0 + - - +
492A ARG* 3.3 28.9 + - - +
493A LEU* 2.9 34.4 + - + +
496A ARG* 6.2 1.3 - - - +
556A CYS 3.9 6.2 - - - +
557A LEU* 3.7 47.0 - - + +
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Residues in contact with LEU 490 (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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440A VAL* 3.8 16.2 - - + -
441A LEU* 3.7 29.4 - - + +
444A MET* 3.8 23.0 - - + +
445A THR* 5.3 0.2 - - + -
486A PHE* 3.1 50.8 + - + +
487A TYR* 3.7 6.1 - - - +
489A GLU* 1.3 75.8 - - - +
491A ILE* 1.3 59.0 + - - +
493A LEU* 3.3 5.9 + - - +
494A ARG* 2.9 29.1 + - - +
500A LEU* 5.6 0.2 - - - +
557A LEU* 4.0 14.6 - - + -
580A ILE* 3.9 28.3 - - + -
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Residues in contact with ILE 491 (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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132A VAL* 4.3 8.7 - - + -
185A LEU* 3.4 41.5 - - + +
186A GLY* 3.6 26.9 - - - +
187A VAL 5.1 0.2 - - - +
444A MET* 3.2 25.8 - - + -
452A ILE* 4.0 20.6 - - + -
487A TYR* 2.9 23.1 + - + +
488A LYS 3.7 4.3 - - - +
490A LEU* 1.3 74.3 - - - +
492A ARG* 1.3 67.0 + - + +
494A ARG* 3.3 2.6 + - - +
495A HIS* 3.1 38.0 + - + +
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Residues in contact with ARG 492 (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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185A LEU 6.0 0.4 - - - +
485A GLU* 5.1 4.4 + - - -
488A LYS* 2.9 47.9 + - + +
489A GLU* 3.3 35.8 + - - +
491A ILE* 1.3 77.6 - - + +
493A LEU* 1.3 64.3 + - - +
495A HIS* 3.0 10.9 + - - +
496A ARG* 2.9 66.2 + - - +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLU* 2.9 27.7 + - + +
490A LEU* 3.5 7.0 - - - +
492A ARG* 1.3 77.4 - - - +
494A ARG* 1.3 62.8 + - - +
496A ARG* 3.0 19.9 + - + +
497A LEU* 2.9 39.2 + - + +
500A LEU* 4.2 6.1 - - + -
556A CYS* 3.7 35.4 - - + +
557A LEU* 3.5 34.1 - - + -
580A ILE* 3.9 18.6 - - + -
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Residues in contact with ARG 494 (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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129A LYS 4.9 2.8 + - - -
130A GLU 6.1 0.4 - - - -
131A ALA 4.7 3.2 + - - -
132A VAL* 4.3 8.7 - - - -
443A GLN 4.1 0.8 + - - -
444A MET* 2.6 52.6 + - - +
445A THR* 3.6 3.6 - - - +
446A TYR 3.4 17.2 + - - -
448A GLY 2.4 33.5 + - - +
450A PRO* 3.5 27.6 - - - +
490A LEU 2.9 17.0 + - - +
491A ILE* 3.6 7.2 - - - +
492A ARG 3.2 0.2 - - - -
493A LEU* 1.3 78.4 - - - +
495A HIS* 1.3 65.2 + - - +
497A LEU 3.4 15.8 - - - +
500A LEU* 3.2 35.9 + - + +
501A THR* 3.6 30.4 + - + +
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Residues in contact with HIS 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 4.2 11.7 + - - -
132A VAL* 3.4 32.9 - - + +
186A GLY* 3.3 22.6 + - - -
188A THR* 3.7 17.4 - - + +
491A ILE* 3.1 18.6 + - + +
492A ARG* 3.0 11.9 + - - +
494A ARG* 1.3 80.5 - - - +
496A ARG* 1.3 62.3 + - + +
497A LEU 5.0 1.0 - - - -
498A ALA* 5.3 0.5 + - - -
501A THR* 5.3 2.8 - - - +
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Residues in contact with ARG 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLU* 6.2 1.2 - - - +
492A ARG* 2.9 60.7 + - - +
493A LEU* 3.0 21.3 + - + +
495A HIS* 1.3 81.5 - - + +
497A LEU* 1.3 67.8 + - + +
498A ALA 3.6 3.3 + - - -
526A GLN* 5.1 2.1 + - - -
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 2.9 24.0 + - + +
494A ARG 3.4 7.6 - - - +
495A HIS 3.6 0.9 - - - -
496A ARG* 1.3 83.6 - - + +
498A ALA* 1.3 60.6 + - - +
499A SER* 3.1 1.8 - - - +
500A LEU* 2.9 51.0 + - + +
501A THR 3.8 1.0 + - - -
526A GLN* 3.7 11.9 - - - +
528A VAL* 4.1 12.1 - - + -
556A CYS* 4.3 15.7 - - - -
580A ILE* 4.2 16.6 - - + -
582A TRP* 3.8 37.7 - - + +
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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
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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