Contacts of the helix formed by residues 486 - 502 (chain A) in PDB entry 1XSK
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 486 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A TYR* 3.0 34.1 + - - +
485A ALA* 1.3 75.3 - - - +
487A TYR* 1.3 64.8 + - - +
488A GLU* 2.9 22.9 - - - +
489A SER* 2.8 30.8 + - - -
490A MET 3.1 15.9 + - - -
517A ASN* 5.5 3.8 - - - +
523A VAL* 4.3 14.4 - - - -
527A TRP* 3.6 8.2 - - - -
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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
----------------------------------------------------------
486A ASN* 1.3 70.7 - - - +
488A GLU* 1.3 74.1 + - - +
490A MET* 2.9 26.8 + - + +
491A ALA* 2.9 13.7 + - - +
522A HIS* 2.8 47.4 + + - +
523A VAL* 3.5 28.8 - - + +
526A ARG* 3.5 24.3 - - + +
619A VAL 4.1 3.8 - - - -
620A PHE* 3.6 32.3 - - + +
621A THR* 3.5 13.2 + - - -
622A GLU* 3.8 15.4 - - + -
158D VAL* 3.8 10.7 - - + +
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Residues in contact with GLU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASN* 2.9 19.7 - - - +
487A TYR* 1.3 80.5 + - - +
489A SER* 1.3 57.5 + - - +
491A ALA* 3.2 5.1 + - - +
492A GLU* 2.9 30.2 + - - +
495A ARG* 5.5 0.3 + - - -
155D ASP* 6.5 0.4 - - + -
156D LEU 3.7 21.8 - - - +
157D GLY* 4.2 14.5 - - - -
158D VAL* 3.8 13.5 + - - +
226D SER* 4.4 19.3 - - - +
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Residues in contact with SER 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 5.7 0.2 - - - -
483A CYS* 3.4 5.0 - - - +
484A TYR* 2.8 48.5 + - - +
486A ASN* 2.8 19.0 + - - -
488A GLU* 1.3 73.6 - - - +
490A MET* 1.3 55.5 + - - +
492A GLU* 3.2 26.0 + - - +
493A SER* 2.5 37.9 + - - -
527A TRP* 4.3 1.1 - - - -
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Residues in contact with MET 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASN 3.1 7.1 + - - +
487A TYR* 2.9 24.0 + - + +
489A SER* 1.3 75.2 - - - +
491A ALA* 1.3 63.4 + - - +
493A SER* 3.2 4.5 + - - -
494A LEU* 3.0 20.6 + - - +
523A VAL 5.0 0.4 - - - +
526A ARG* 4.5 4.0 - - + +
527A TRP* 3.6 67.3 - - + -
530A PHE* 3.8 19.3 - - + -
618A PRO* 4.5 8.1 - - + -
619A VAL 3.3 21.1 - - - +
620A PHE* 3.2 36.3 - - + -
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A TYR 2.9 10.1 + - - +
488A GLU* 3.3 9.0 - - - +
490A MET* 1.3 73.3 - - - +
492A GLU* 1.3 59.6 + - - +
494A LEU* 2.7 25.6 + - - +
495A ARG* 3.0 26.0 + - + +
605A ASP 5.3 0.2 - - - +
606A ARG* 5.8 3.6 - - + -
620A PHE* 3.6 21.9 - - + -
158D VAL* 4.1 23.8 - - + -
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Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 3.5 14.2 - - - +
188A THR* 2.7 45.7 + - - +
189A SER* 3.1 15.3 + - - -
488A GLU* 2.9 13.1 + - - +
489A SER* 3.2 32.3 + - - +
491A ALA* 1.3 74.8 - - - +
493A SER* 1.3 65.6 + - - +
495A ARG* 3.3 34.7 + - - +
496A GLY 3.2 16.5 + - - -
225D VAL* 3.4 15.9 - - + +
226D SER* 4.6 7.7 + - - -
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Residues in contact with SER 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 4.5 9.6 - - - -
188A THR* 4.7 2.5 + - - +
480A GLY* 6.1 1.6 - - - -
483A CYS* 3.5 23.5 - - - +
489A SER 2.5 23.3 + - - -
490A MET* 3.3 9.2 - - - -
491A ALA 3.0 0.6 - - - -
492A GLU* 1.3 78.4 - - - +
494A LEU* 1.3 63.7 + - - +
496A GLY* 3.3 2.1 + - - +
497A GLY 3.1 8.3 + - - -
508A TRP* 2.8 32.4 - - - -
510A HIS* 5.2 5.8 - - - -
527A TRP* 4.4 6.6 - - - -
530A PHE* 5.1 3.6 - - - -
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Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A MET 3.0 9.5 + - - +
491A ALA* 2.7 19.0 + - - +
493A SER* 1.3 70.3 - - - +
495A ARG* 1.3 58.1 + - - +
497A GLY 3.1 1.2 + - - -
498A LEU* 2.9 35.0 + - + +
508A TRP* 4.2 0.9 - - - -
530A PHE* 3.7 31.2 - - + -
588A MET* 3.9 13.9 - - - -
605A ASP 3.6 21.5 - - - +
606A ARG* 3.9 23.1 - - - +
607A GLN 4.3 0.4 - - - +
608A TYR* 3.8 25.6 - - + -
618A PRO* 4.4 8.3 - - + -
620A PHE* 4.1 14.4 - - + -
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Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG 3.8 4.0 - - - +
169A PHE 2.7 28.0 + - - +
170A THR 3.3 22.7 + - - +
171A ALA* 4.3 4.0 - - - +
172A LEU* 4.0 15.6 - - + +
488A GLU 5.5 0.2 + - - -
491A ALA* 3.0 21.2 + - + +
492A GLU* 3.5 30.8 - - - +
494A LEU* 1.3 75.5 - - - +
496A GLY* 1.3 59.0 + - - +
498A LEU* 3.7 9.4 - - - +
499A SER* 2.8 34.0 + - - +
605A ASP* 3.4 36.4 + - + +
225D VAL* 3.6 20.2 + - - +
226D SER* 5.8 1.2 - - - +
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Residues in contact with GLY 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 3.8 11.1 - - - +
168A ARG 3.2 19.0 + - - -
169A PHE* 4.1 17.3 - - - -
492A GLU 3.2 7.3 + - - -
493A SER 3.3 3.5 + - - -
494A LEU 3.2 0.8 - - - -
495A ARG* 1.3 80.2 - - - +
497A GLY* 1.3 56.3 + - - +
499A SER* 3.4 1.8 + - - -
500A ILE* 3.0 30.1 + - - +
508A TRP* 4.4 1.3 - - - -
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Residues in contact with GLY 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER 3.1 11.1 + - - -
494A LEU 3.1 1.3 + - - -
496A GLY* 1.3 75.9 - - - +
498A LEU* 1.3 62.9 + - - +
500A ILE* 3.0 18.1 - - - +
501A GLY* 3.3 4.2 + - - -
508A TRP* 3.3 46.1 - - - +
588A MET* 4.6 9.2 - - - +
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.0 17.9 - - + -
494A LEU* 2.9 24.4 + - + +
495A ARG* 3.7 3.4 - - - +
497A GLY* 1.3 75.7 - - - +
499A SER* 1.3 63.1 + - - +
501A GLY* 3.0 12.3 + - - -
502A LEU* 3.1 18.0 + - - +
588A MET* 4.0 15.8 - - + +
589A ARG* 4.0 2.0 - - - -
590A ALA* 3.9 27.0 + - + +
593A MET* 5.6 0.3 - - - +
604A LEU 4.4 1.8 - - - +
605A ASP* 3.5 39.5 - - + +
607A GLN 4.1 8.3 - - - +
608A TYR* 3.6 28.7 - - + -
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Residues in contact with SER 499 (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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164A GLY* 4.2 3.1 + - - -
166A GLY 3.4 17.7 - - - +
168A ARG 3.7 11.2 + - - -
172A LEU* 3.4 13.0 - - - +
174A ARG* 3.2 24.7 + - - -
495A ARG 2.8 26.2 + - - -
496A GLY 3.6 4.0 - - - -
498A LEU* 1.3 73.1 - - - +
500A ILE* 1.3 57.7 + - - +
502A LEU* 3.0 29.2 + - - +
503A SER* 3.2 14.7 + - - -
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Residues in contact with ILE 500 (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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166A GLY 3.9 4.0 + - - -
167A GLU* 3.9 19.7 - - + +
195A LYS* 3.7 31.0 - - + -
478A HIS* 4.3 9.2 - - + -
496A GLY 3.0 14.9 + - - +
497A GLY* 3.0 25.6 - - - +
499A SER* 1.3 77.3 - - - +
501A GLY* 1.3 61.6 + - - +
503A SER* 3.1 12.6 + - - -
505A PHE* 3.1 56.0 + - + +
507A PHE 5.7 0.7 - - - +
508A TRP* 4.0 19.5 - - + -
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Residues in contact with GLY 501 (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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251A LEU* 3.7 9.0 - - - +
497A GLY 3.3 3.7 + - - -
498A LEU 3.0 8.3 + - - -
500A ILE* 1.3 79.1 - - - +
502A LEU* 1.3 58.7 + - - +
503A SER 3.0 9.0 + - - -
504A GLY* 3.4 10.2 + - - -
505A PHE 3.3 17.3 - - - -
586A PRO* 3.7 28.1 - - - +
588A MET 4.8 3.6 - - - -
593A MET* 4.4 1.8 - - - -
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Residues in contact with LEU 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 3.7 32.1 - - + -
164A GLY* 4.3 13.1 - - - +
172A LEU* 4.3 7.9 - - + -
199A PHE* 3.5 20.8 - - - -
201A MET* 4.0 24.3 - - + +
251A LEU* 3.9 6.2 - - - +
498A LEU 3.1 17.7 + - - +
499A SER* 3.0 16.7 + - - +
501A GLY* 1.3 77.4 - - - +
503A SER* 1.3 55.7 + - - +
504A GLY 3.6 0.9 - - - -
590A ALA* 4.1 17.3 - - + -
592A MET* 4.0 22.2 - - - -
593A MET* 3.7 23.8 - - + -
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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