Contacts of the helix formed by residues 520 - 532 (chain D) in PDB entry 1CX2
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 GLU 520 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D THR* 5.4 0.5 - - - +
86D PRO* 3.8 19.8 - - + +
87D ASN* 4.2 17.8 + - - +
467D ARG* 2.7 44.1 + - - +
472D LEU* 3.9 8.4 - - + +
473D LYS 5.0 0.5 + - - -
475D TYR* 3.1 12.6 + - - -
510D GLU* 3.8 3.2 + - - +
511D LYS 4.7 1.2 + - - -
513D ARG* 3.8 31.5 - - + +
519D GLY* 1.3 69.1 - - - -
521D THR* 1.3 55.6 + - - +
523D VAL* 3.0 2.8 + - - -
524D GLU* 2.7 50.9 + - + +
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Residues in contact with THR 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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463D LEU* 4.0 24.4 - - + +
466D TYR* 6.4 0.4 - - + -
467D ARG* 2.5 41.5 + - + +
472D LEU* 4.1 5.6 - - + -
475D TYR* 3.8 3.5 + - - -
503D LEU* 4.6 8.1 - - + -
507D LEU* 3.8 16.2 - - + -
510D GLU* 3.1 23.3 + - + -
520D GLU* 1.3 79.6 - - - +
522D MET* 1.3 65.1 + - - +
524D GLU* 4.2 0.2 - - - -
525D LEU* 3.3 26.4 + - + +
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Residues in contact with MET 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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384D LEU* 3.4 32.7 - - + +
387D TRP* 2.9 38.1 - - + +
434D VAL* 3.6 22.0 - - + -
507D LEU* 3.2 33.2 - - + +
508D LEU* 4.7 7.4 - - + -
510D GLU* 3.8 2.7 + - - +
518D PHE* 3.5 34.5 - - + -
519D GLY 3.3 9.3 + - - +
520D GLU 3.3 0.4 - - - -
521D THR* 1.3 81.8 - - - +
523D VAL* 1.3 64.0 + - - +
525D LEU* 4.1 1.6 - - - +
526D GLY* 3.2 21.0 + - - -
701D S58 4.5 2.4 - - + -
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Residues in contact with VAL 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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513D ARG* 3.1 25.8 - - - +
518D PHE* 3.3 13.7 - - + -
519D GLY 3.3 16.2 - - - +
520D GLU 3.0 3.0 + - - +
522D MET* 1.3 80.0 - - - +
524D GLU* 1.3 62.9 + - - +
527D ALA* 3.2 27.8 + - + +
701D S58 3.1 70.6 - - + +
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Residues in contact with GLU 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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86D PRO* 3.6 19.7 - - + +
120D ARG* 5.1 14.3 + - - -
470D PHE* 3.7 11.6 - - + +
472D LEU* 3.4 39.0 - - + +
513D ARG* 3.5 16.0 + - - +
520D GLU* 2.7 30.0 + - + +
523D VAL* 1.3 82.9 - - - +
525D LEU* 1.3 58.8 + - - +
527D ALA* 5.0 2.1 - - - +
528D PRO* 2.9 28.1 - - - +
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Residues in contact with LEU 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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380D GLU* 5.1 4.0 - - + -
384D LEU* 3.6 21.1 - - + -
466D TYR* 3.9 28.9 - - + +
467D ARG 5.1 0.2 - - - +
470D PHE* 3.2 46.0 - - + -
472D LEU* 4.6 7.0 - - + -
503D LEU* 3.4 37.7 - - + -
507D LEU* 5.6 0.7 - - + -
521D THR* 3.3 21.2 + - + +
524D GLU* 1.3 76.7 - - - +
526D GLY* 1.3 60.5 + - - +
528D PRO* 3.5 4.5 - - - +
529D PHE* 3.4 28.3 - - + -
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Residues in contact with GLY 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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381D PHE* 3.4 18.8 - - - -
384D LEU* 4.1 6.0 - - - +
522D MET 3.2 8.9 + - - -
525D LEU* 1.3 77.7 - - - +
527D ALA* 1.3 58.7 + - - +
528D PRO 3.3 2.0 - - - -
529D PHE 3.8 0.2 - - - -
530D SER* 2.7 34.5 + - - -
701D S58 3.4 19.3 - - - -
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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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120D ARG* 3.3 28.3 - - - +
523D VAL* 3.2 21.8 + - + +
524D GLU* 4.6 3.1 - - - +
526D GLY* 1.3 73.6 - - - +
528D PRO* 1.4 72.2 - - + +
530D SER* 3.2 1.4 + - - -
531D LEU* 3.1 27.0 + - - +
701D S58 3.3 29.6 - - + -
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Residues in contact with PRO 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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120D ARG* 3.3 33.2 - - + +
121D SER* 3.3 18.0 + - - +
123D LEU* 4.3 6.3 - - + -
124D ILE* 3.5 24.5 - - + +
470D PHE* 4.3 11.9 - - + -
524D GLU 2.9 24.9 - - - +
525D LEU 3.5 5.6 - - - +
526D GLY 3.4 2.7 - - - -
527D ALA* 1.4 94.1 - - + +
529D PHE* 1.3 65.2 + - + +
531D LEU 3.4 6.1 + - - -
532D LYS* 3.4 6.2 + - - +
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Residues in contact with PHE 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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123D LEU 4.8 2.0 - - - -
124D ILE* 3.9 25.4 - - + -
151D ALA* 3.4 20.4 - - + -
375D ASN* 4.9 2.9 - - - +
378D ALA* 4.0 11.4 - - + -
380D GLU* 3.8 23.8 - - + -
381D PHE* 2.9 55.9 - + + -
384D LEU* 5.0 1.8 - - + -
470D PHE* 3.2 36.1 - + - -
525D LEU* 3.4 15.9 - - + +
526D GLY 3.3 2.8 + - - +
528D PRO* 1.3 83.9 - - - +
530D SER* 1.3 57.9 + - - +
531D LEU 3.4 0.7 + - - -
532D LYS* 3.8 2.6 + - - +
533D GLY* 3.7 14.9 + - - -
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Residues in contact with SER 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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205D PHE* 5.3 5.7 - - - -
209D PHE* 5.9 1.2 - - - -
344D VAL* 5.6 1.6 - - - +
348D TYR* 5.8 1.6 - - - -
349D VAL* 5.5 4.1 - - - +
381D PHE* 3.5 20.8 - - - -
385D TYR* 4.2 10.0 + - - -
526D GLY 2.7 21.6 + - - -
527D ALA 3.2 3.3 + - - -
529D PHE* 1.3 74.5 - - - +
531D LEU* 1.3 60.7 + - - +
533D GLY* 4.2 1.6 - - - -
534D LEU* 3.0 41.7 + - - +
701D S58 4.1 18.6 - - - -
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Residues in contact with LEU 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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113D MET* 5.8 0.4 - - + -
116D VAL 4.4 2.0 - - - +
117D LEU* 3.9 30.3 - - + +
120D ARG* 3.7 23.3 - - + -
121D SER* 3.8 9.9 - - - +
345D ILE* 3.8 28.5 - - + -
349D VAL* 5.3 4.9 - - + -
371D PHE* 6.1 0.2 - - - -
527D ALA 3.1 12.4 + - - +
528D PRO 3.4 0.2 + - - -
529D PHE 3.3 0.4 - - - -
530D SER* 1.3 77.9 - - - +
532D LYS* 1.3 53.4 + - - +
533D GLY 3.1 4.7 - - - -
534D LEU* 3.0 6.8 + - + +
535D MET* 2.7 41.3 + - + +
701D S58 3.5 37.9 - - + -
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Residues in contact with LYS 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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121D SER* 3.6 28.5 - - - +
124D ILE* 3.8 30.3 - - + +
126D SER* 3.7 20.2 - - - -
371D PHE* 3.7 22.8 - - + -
372D GLN* 2.7 36.5 + - - +
374D GLN 3.3 19.0 + - - +
375D ASN* 3.5 21.4 - - - +
528D PRO 3.4 9.3 + - - +
529D PHE* 4.5 2.5 - - - +
531D LEU* 1.3 76.1 - - - +
533D GLY* 1.3 58.0 + - - +
536D GLY* 3.3 25.7 + - - +
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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