Contacts of the helix formed by residues 486 - 502 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484E TYR* 3.2 22.2 + - - +
485E ALA* 1.3 75.6 - - - +
487E TYR* 1.3 63.5 + - - +
488E GLU* 3.6 17.0 - - - +
489E SER* 2.8 37.2 + - - -
490E MET* 3.1 20.8 + - - +
517E ASN* 6.0 1.0 - - - +
523E VAL* 4.2 13.5 - - - -
527E TRP* 3.8 3.1 - - - -
133F GLN* 5.7 4.8 - - - +
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Residues in contact with TYR 487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486E ASN* 1.3 70.9 - - - +
488E GLU* 1.3 71.7 + - - +
490E MET* 3.1 33.1 + - + +
491E ALA* 2.9 23.4 + - - +
522E HIS* 2.7 43.3 + + - -
523E VAL* 3.4 28.2 - - + +
526E ARG* 3.6 12.5 - - + +
620E PHE* 3.4 28.4 - - + +
621E THR* 3.6 10.3 + - - -
622E GLU* 3.6 20.4 + - + -
158F VAL* 3.8 13.5 - - + +
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Residues in contact with GLU 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486E ASN* 3.6 18.3 - - - +
487E TYR* 1.3 85.9 + - - +
489E SER* 1.3 58.4 + - - +
491E ALA* 3.2 4.4 + - - +
492E GLU* 3.0 30.5 + - - +
495E ARG* 5.3 0.9 + - - -
156F LEU 3.5 22.9 - - - +
157F GLY* 4.0 15.6 - - - -
158F VAL* 4.1 14.2 + - - +
226F SER* 4.2 19.3 - - - +
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Residues in contact with SER 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483E CYS* 3.3 7.4 - - - +
484E TYR* 2.8 46.4 + - - -
486E ASN* 2.8 21.7 + - - -
488E GLU* 1.3 74.0 - - - +
490E MET* 1.3 57.3 + - - +
492E GLU* 3.1 24.3 + - - +
493E SER* 2.5 34.9 + - - -
527E TRP* 4.3 0.4 - - - -
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Residues in contact with MET 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486E ASN 3.1 12.6 + - - +
487E TYR* 3.1 41.6 + - + +
489E SER* 1.3 76.0 - - - +
491E ALA* 1.3 61.4 + - - +
493E SER* 3.3 5.4 + - - -
494E LEU* 3.2 18.9 + - - +
523E VAL* 4.8 1.6 - - - +
526E ARG* 4.3 2.7 - - + +
527E TRP* 3.6 63.0 - - + -
530E PHE* 4.1 20.1 - - + -
618E PRO* 5.5 1.1 - - + -
619E VAL 3.6 14.6 - - - +
620E PHE* 3.1 35.8 - - + -
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Residues in contact with ALA 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487E TYR 2.9 12.1 + - - +
488E GLU* 3.4 9.4 - - - +
490E MET* 1.3 73.3 - - - +
492E GLU* 1.3 65.6 + - - +
493E SER 3.0 1.3 - - - -
494E LEU* 3.0 15.3 + - - +
495E ARG* 3.1 27.1 + - - +
605E ASP 5.2 0.5 - - - +
606E ARG* 5.8 4.5 - - + -
620E PHE* 3.8 19.9 - - + -
158F VAL* 4.2 22.4 - - + -
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Residues in contact with GLU 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E PHE* 3.5 16.5 - - - +
188E THR* 3.3 32.6 + - - +
189E SER* 3.4 18.0 - - - -
484E TYR* 5.0 1.4 + - - -
488E GLU 3.0 16.0 + - - +
489E SER* 3.1 40.5 + - - +
491E ALA* 1.3 74.5 - - - +
493E SER* 1.3 65.9 + - - +
495E ARG* 3.3 34.2 + - - +
496E GLY 3.0 16.3 + - - -
225F VAL* 3.4 14.8 - - + +
226F SER* 4.3 9.0 + - - -
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Residues in contact with SER 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E PHE* 4.4 9.4 - - - -
188E THR* 5.0 1.8 + - - -
480E GLY* 6.3 1.3 - - - -
483E CYS* 3.7 21.1 - - - +
489E SER 2.5 23.6 + - - -
490E MET* 3.3 10.8 - - - -
491E ALA 3.0 0.4 - - - -
492E GLU* 1.3 80.3 - - - +
494E LEU* 1.3 56.9 + - - +
496E GLY* 3.0 3.0 + - - +
497E GLY 2.9 23.6 + - - -
508E TRP* 3.2 21.7 - - - -
510E HIS* 5.2 5.6 - - - -
527E TRP* 4.1 8.1 - - - -
530E PHE* 5.1 3.1 - - - -
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Residues in contact with LEU 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490E MET 3.2 6.9 + - - +
491E ALA* 3.0 10.6 + - - +
493E SER* 1.3 78.4 - - - +
495E ARG* 1.3 57.3 + - - +
497E GLY 3.1 1.5 + - - +
498E LEU* 2.8 41.7 + - + +
508E TRP* 4.4 1.6 - - - -
530E PHE* 3.8 28.2 - - + -
588E MET* 3.9 10.3 - - - -
605E ASP 3.4 23.8 - - - +
606E ARG* 3.8 23.1 - - - +
607E GLN 4.1 2.0 - - - +
608E TYR* 3.8 28.5 - - + -
618E PRO* 4.5 6.5 - - + -
620E PHE* 4.3 12.8 - - + -
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Residues in contact with ARG 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E ARG 3.8 3.6 - - - +
169E PHE* 2.9 21.9 + - - -
170E THR 3.1 31.8 + - - +
171E ALA* 4.3 3.8 - - - +
172E LEU* 3.9 18.1 - - + +
488E GLU 5.3 0.8 + - - -
491E ALA* 3.1 19.8 + - - +
492E GLU* 3.5 30.6 - - - +
494E LEU* 1.3 76.0 - - - +
496E GLY* 1.3 58.9 + - - +
498E LEU* 3.4 8.8 + - - +
499E SER* 2.8 33.8 + - - -
605E ASP* 3.5 36.2 + - + +
159F GLY 6.1 0.4 - - - +
225F VAL* 3.9 18.6 + - - +
226F SER* 5.9 0.8 - - - +
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Residues in contact with GLY 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E GLU* 3.8 12.1 - - - +
168E ARG 3.2 18.1 + - - -
169E PHE* 4.0 17.7 - - - -
492E GLU 3.0 7.5 + - - -
493E SER 3.0 8.4 + - - -
495E ARG* 1.3 77.9 - - - +
497E GLY* 1.3 61.1 + - - +
499E SER* 3.2 3.8 + - - -
500E ILE* 3.0 23.6 + - - +
508E TRP* 4.5 0.4 - - - -
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Residues in contact with GLY 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493E SER 2.9 11.7 + - - -
494E LEU 3.1 2.9 + - - -
496E GLY* 1.3 73.5 - - - +
498E LEU* 1.3 65.8 + - - +
500E ILE* 3.1 20.4 - - - +
501E GLY* 3.3 2.9 + - - -
508E TRP* 3.3 42.8 - - - +
588E MET* 4.8 8.6 - - - +
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Residues in contact with LEU 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E LEU* 3.9 15.7 - - + -
494E LEU* 2.8 29.7 + - + +
495E ARG* 3.8 3.6 - - - +
497E GLY* 1.3 71.2 - - - -
499E SER* 1.3 63.2 + - - +
501E GLY* 3.1 3.8 + - - -
502E LEU* 3.1 25.9 + - - +
588E MET* 3.9 22.0 - - + +
589E ARG 4.1 0.2 - - - -
590E ALA* 4.0 25.9 - - + +
593E MET* 5.5 1.2 - - - +
604E LEU 4.4 5.2 - - - +
605E ASP* 3.7 33.0 - - + +
607E GLN 4.0 13.2 - - - +
608E TYR* 3.7 24.5 - - + -
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Residues in contact with SER 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E GLY* 4.4 2.5 + - - -
166E GLY 3.3 20.0 - - - -
168E ARG 3.8 11.8 + - - -
172E LEU* 3.5 12.5 - - - +
174E ARG* 3.5 21.0 + - - -
495E ARG* 2.8 23.5 + - - +
496E GLY 3.5 4.3 - - - -
498E LEU* 1.3 77.5 - - - +
500E ILE* 1.3 61.8 + - - +
502E LEU* 3.1 13.8 + - - +
503E SER* 2.8 26.2 + - - -
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Residues in contact with ILE 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLY* 4.1 3.7 + - - -
167E GLU* 3.8 20.9 - - + +
195E LYS* 3.8 28.5 - - + -
478E HIS* 4.0 12.1 - - + +
496E GLY 3.0 12.4 + - - +
497E GLY 3.1 15.3 - - - +
499E SER* 1.3 75.9 - - - +
501E GLY* 1.3 63.9 + - - +
503E SER* 2.9 20.8 + - - -
504E GLY 3.4 0.5 + - - -
505E PHE* 3.1 59.1 + - + +
507E PHE 5.2 1.1 - - - +
508E TRP* 3.9 27.6 - - + -
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Residues in contact with GLY 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E LEU* 3.6 14.7 - - - +
497E GLY 3.3 2.3 + - - -
498E LEU 3.1 7.5 + - - -
500E ILE* 1.3 79.0 - - - +
502E LEU* 1.3 58.9 + - - +
503E SER 2.9 9.2 + - - -
504E GLY* 3.3 10.6 + - - -
505E PHE 3.3 18.3 + - - -
586E PRO* 3.6 25.7 - - - +
588E MET 4.9 3.1 - - - -
593E MET* 4.6 0.4 - - - -
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Residues in contact with LEU 502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E TYR* 3.8 37.5 - - + -
164E GLY* 4.4 7.5 - - - +
172E LEU* 4.4 8.3 - - + -
199E PHE* 3.6 18.7 - - - -
201E MET* 3.9 23.4 - - - +
247E PRO* 5.6 0.2 - - + -
251E LEU* 3.9 10.2 - - - +
498E LEU 3.1 22.4 + - - +
499E SER* 3.1 12.5 + - - +
501E GLY* 1.3 74.9 - - - +
503E SER* 1.3 57.6 + - - +
504E GLY 3.5 0.7 - - - -
590E ALA* 4.0 17.7 - - + -
592E MET* 3.7 26.5 - - - -
593E MET* 4.1 20.6 - - + -
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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