Contacts of the helix formed by residues 520 - 532 (chain D) in PDB entry 2XNS
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 SER 520 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B GLY* 6.4 0.2 - - - -
180B LYS* 5.8 1.7 + - - -
518D LEU 3.2 8.2 + - - -
519D LEU* 1.3 74.9 - - - +
521D ASN* 1.3 60.5 + - - +
522D GLU* 4.0 7.6 + - - +
523D GLU* 3.0 39.4 + - - +
524D VAL* 3.1 16.4 + - - +
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Residues in contact with ASN 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLY* 4.6 21.2 - - - +
519D LEU 4.9 2.1 - - - +
520D SER* 1.3 76.5 - - - +
522D GLU* 1.3 57.2 + - - +
524D VAL* 3.3 8.5 + - - +
525D PHE* 2.9 30.7 + - - +
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Residues in contact with GLU 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D SER* 3.2 7.3 - - - +
521D ASN* 1.3 78.9 - - - +
523D GLU* 1.3 61.7 + - - +
525D PHE* 3.3 31.9 + - - +
526D ARG* 3.2 23.7 + - - +
529D ARG* 5.3 0.7 + - - -
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Residues in contact with GLU 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLN* 3.0 36.2 + - - -
82B ILE* 5.7 3.1 - - + -
180B LYS* 6.1 0.7 - - - -
514D ASP* 3.5 38.1 - - + +
516D ARG 4.8 1.4 - - - +
518D LEU 4.1 2.2 - - - +
519D LEU* 3.4 28.7 - - + +
520D SER* 3.0 19.8 + - - +
522D GLU* 1.3 77.9 - - - +
524D VAL* 1.3 59.6 + - - +
526D ARG* 3.5 4.6 + - - +
527D ALA* 3.1 26.7 + - - +
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Residues in contact with VAL 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 5.1 5.4 - - + -
108B PHE* 3.6 44.1 - - + +
111B ALA* 3.8 17.0 - - + -
112B GLY* 4.7 7.6 - - - +
519D LEU* 3.7 28.7 - - + -
520D SER 3.1 15.6 + - - +
521D ASN* 3.3 8.5 + - - +
523D GLU* 1.3 73.4 - - - +
525D PHE* 1.3 60.2 + - - +
527D ALA* 3.4 6.5 + - - +
528D LEU* 3.0 27.1 + - + +
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Residues in contact with PHE 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D ASN 2.9 18.2 + - - +
522D GLU* 3.3 31.6 - - - +
524D VAL* 1.3 74.4 - - - +
526D ARG* 1.3 62.2 + - + +
528D LEU* 3.1 13.3 + - + +
529D ARG* 2.8 72.9 + - + +
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Residues in contact with ARG 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 3.3 37.1 + - - +
90B ARG* 5.0 5.3 - - - +
514D ASP* 4.6 10.8 + - - -
522D GLU* 3.2 15.9 + - - +
523D GLU* 4.1 4.7 - - - +
525D PHE* 1.3 85.1 - - + +
527D ALA* 1.3 61.4 + - - +
529D ARG* 3.0 43.1 - - - +
530D ASP* 3.2 23.9 + - - +
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Residues in contact with ALA 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 3.6 32.3 - - + -
86B ARG* 4.3 14.7 - - - +
108B PHE* 3.8 15.8 - - + -
523D GLU* 3.1 15.3 + - + +
524D VAL* 3.4 12.6 - - - +
525D PHE 3.1 0.2 - - - -
526D ARG* 1.3 79.4 - - - +
528D LEU* 1.3 56.1 + - - +
530D ASP* 3.7 5.5 + - - +
531D PHE* 3.1 25.3 + - - +
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Residues in contact with LEU 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 6.1 3.4 - - + -
108B PHE* 3.9 36.1 - - + +
109B VAL* 6.4 1.1 - - + -
524D VAL* 3.0 13.9 + - + +
525D PHE* 3.1 15.0 + - + +
527D ALA* 1.3 74.5 - - - +
529D ARG* 1.3 67.5 + - - +
531D PHE* 2.9 19.0 + - + +
532D ASP* 3.0 36.4 + - - +
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Residues in contact with ARG 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D GLU* 5.3 0.8 + - - -
525D PHE* 2.8 59.2 + - + +
526D ARG* 3.0 47.5 - - - +
528D LEU* 1.3 75.1 - - - +
530D ASP* 1.3 64.6 + - - +
532D ASP* 3.4 16.4 + - - +
533D ARG* 3.8 35.7 + - - +
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Residues in contact with ASP 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 3.6 59.2 + - - +
89B GLY* 5.8 2.7 - - - -
90B ARG* 5.3 3.0 + - - -
526D ARG* 3.2 16.2 + - - +
527D ALA 3.7 3.8 - - - +
528D LEU 3.2 0.4 - - - -
529D ARG* 1.3 81.5 - - - +
531D PHE* 1.3 67.2 + - - +
533D ARG* 3.0 33.9 + - - +
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Residues in contact with PHE 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ILE* 3.8 22.4 - - + -
95B PHE* 4.1 15.3 - + - -
101B ALA* 3.9 23.3 - - + -
104B ALA* 3.5 29.2 - - + -
105B ARG* 4.1 24.7 - - + -
108B PHE* 3.7 23.8 - + + -
527D ALA 3.1 11.6 + - - +
528D LEU* 2.9 8.6 + - + +
530D ASP* 1.3 82.7 + - - +
532D ASP* 1.3 66.1 + - - +
533D ARG 2.9 6.9 + - - -
534D TRP 3.0 36.5 - - - +
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Residues in contact with ASP 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 5.3 5.7 + - - +
528D LEU* 3.0 33.7 + - - +
529D ARG* 3.6 12.3 - - - +
530D ASP 3.1 1.0 + - - -
531D PHE* 1.3 83.0 - - - +
533D ARG* 1.3 63.3 + - + +
534D TRP 4.2 0.7 - - - -
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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
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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