Contacts of the helix formed by residues 515 - 527 (chain B) in PDB entry 1COZ
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 TRP 515 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A HIS* 4.2 12.5 - + - -
54A HIS* 3.1 56.1 + + + +
57A LEU* 4.0 26.0 - - + -
58A ILE* 3.6 5.7 - - + +
514B HIS* 1.3 75.3 - - + +
516B GLY* 1.3 65.4 + - - +
518B ILE* 3.7 11.8 - - - +
519B LYS* 3.1 30.6 + - + +
614B THR* 3.3 30.1 - - + -
615B GLU 3.7 17.9 - - - -
616B GLY* 4.2 7.2 - - - -
617B ILE* 3.4 33.6 - - + +
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Residues in contact with GLY 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B HIS* 3.1 19.1 + - - -
515B TRP* 1.3 79.0 - - - +
517B HIS* 1.3 65.2 + - - +
519B LYS* 3.5 2.3 + - - +
520B LEU* 3.2 21.8 + - - +
523B ARG* 5.2 0.2 + - - -
614B THR* 3.8 26.2 + - - -
617B ILE* 4.1 4.3 - - - -
630B CTP 3.9 12.9 - - - +
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Residues in contact with HIS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B PHE* 3.7 31.3 - + + -
511B ASP 4.2 1.1 - - - -
512B LEU 3.9 4.5 - - - -
513B LEU* 3.5 23.2 - - + +
514B HIS* 3.0 49.3 + + - +
516B GLY* 1.3 78.4 - - - +
518B ILE* 1.3 56.4 + - - +
520B LEU* 3.3 7.6 + - - +
521B LEU* 3.0 33.1 + - + +
619B THR* 3.5 11.4 - - - -
630B CTP 2.6 53.2 + + - -
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Residues in contact with ILE 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 3.7 16.8 - - + -
58A ILE* 3.8 23.8 - - + -
61A THR* 3.7 39.9 - - + +
513B LEU* 4.3 17.7 - - + -
514B HIS 3.2 11.8 + - - +
515B TRP 3.7 6.7 - - - +
516B GLY 3.3 0.2 - - - -
517B HIS* 1.3 77.6 - - - +
519B LYS* 1.3 58.1 + - + +
521B LEU* 3.2 8.0 + - + +
522B GLU* 2.8 32.4 + - - +
562B ILE* 4.2 22.4 - - + -
564B TYR* 4.2 9.0 - - + +
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Residues in contact with LYS 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 5.8 8.3 - - + -
515B TRP* 3.1 21.7 + - + +
516B GLY 3.9 1.1 - - - +
517B HIS 3.4 0.2 - - - -
518B ILE* 1.3 74.6 - - + +
520B LEU* 1.3 64.5 + - - +
522B GLU* 3.3 32.9 + - - +
523B ARG* 3.0 59.5 + - - +
614B THR* 3.8 21.3 - - + +
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B THR* 4.0 31.2 - - + +
510B PHE* 4.5 9.4 - - + -
516B GLY 3.2 13.3 + - - +
517B HIS 3.4 8.3 - - - +
518B ILE 3.2 0.2 - - - -
519B LYS* 1.3 75.0 - - - +
521B LEU* 1.3 71.7 + - + +
523B ARG* 3.2 15.6 + - - +
524B ALA* 2.8 33.9 + - + +
590B VAL* 4.8 5.6 - - + -
592B GLY* 5.2 4.5 - - - +
611B LEU* 3.8 27.8 - - + +
630B CTP 4.0 38.6 - - - +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B THR* 4.5 2.2 - - + -
510B PHE* 4.2 23.1 - - + -
513B LEU* 5.1 1.3 - - + -
517B HIS 3.0 21.2 + - - +
518B ILE* 3.6 12.3 - - + +
520B LEU* 1.3 84.0 - - + +
522B GLU* 1.3 62.6 + - - +
524B ALA* 4.5 0.7 - - - -
525B LYS* 3.1 26.2 + - - +
531B LEU* 3.7 13.9 - - + +
533B VAL* 3.9 27.1 - - + -
559B LEU* 3.8 25.4 - - + -
562B ILE* 4.3 12.8 - - + -
564B TYR* 3.8 16.9 - - + +
565B VAL* 4.0 10.5 - - + -
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Residues in contact with GLU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B ILE* 2.8 19.5 + - - +
519B LYS* 3.3 39.4 + - - +
521B LEU* 1.3 78.9 - - - +
523B ARG* 1.3 63.3 + - + +
525B LYS* 3.8 2.4 - - - +
526B GLN* 3.2 27.7 + - - +
564B TYR* 3.6 39.1 + - + +
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Residues in contact with ARG 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B GLY 5.2 0.2 + - - -
519B LYS* 3.0 45.4 + - - +
520B LEU* 3.8 23.2 - - - +
522B GLU* 1.3 74.4 - - + +
524B ALA* 1.3 64.9 + - - +
526B GLN* 3.1 33.9 + - + +
527B LEU* 3.7 12.6 + - - +
611B LEU* 3.8 27.8 - - + +
612B PRO* 2.8 51.5 + - - +
614B THR* 4.5 10.6 + - - -
630B CTP 4.2 9.9 + - - -
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Residues in contact with ALA 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B VAL* 3.7 13.9 - - + +
506B THR* 5.0 2.5 - - + -
520B LEU* 2.8 28.0 + - + +
521B LEU* 4.0 4.3 - - - +
523B ARG* 1.3 70.0 - - - +
525B LYS* 1.3 67.2 + - - +
527B LEU* 3.1 27.3 + - - +
531B LEU* 4.0 20.6 - - + -
590B VAL* 4.4 22.2 - - + -
611B LEU* 4.1 3.3 - - - +
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Residues in contact with LYS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B VAL* 5.3 0.7 - - - -
521B LEU 3.1 19.5 + - - +
522B GLU 3.8 4.0 - - - +
523B ARG 3.3 0.2 - - - -
524B ALA* 1.3 76.6 - - - +
526B GLN* 1.3 59.4 + - - +
527B LEU 2.9 5.8 + - - -
528B GLY* 3.0 22.3 + - - +
529B ASP* 3.5 24.4 + - - +
530B TYR 4.5 0.9 - - - -
531B LEU* 3.9 18.1 - - + +
563B ARG 4.3 5.3 + - - -
564B TYR* 3.4 43.4 + - + +
566B ASP* 2.8 30.9 + - - -
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Residues in contact with GLN 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B GLU* 3.2 16.9 + - + +
523B ARG* 3.1 37.7 - - + +
524B ALA 3.2 0.6 - - - -
525B LYS* 1.3 74.1 - - - +
527B LEU* 1.3 69.4 + - + +
528B GLY 3.3 3.0 + - - +
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B LYS* 3.7 24.0 + - - +
504B VAL* 3.9 3.6 - - + -
523B ARG 3.7 17.0 - - - +
524B ALA* 3.1 9.8 + - - +
525B LYS 2.9 1.4 + - - -
526B GLN* 1.3 92.4 - - + +
528B GLY* 1.3 55.7 + - - +
588B VAL* 3.8 20.0 - - + +
590B VAL* 3.9 24.9 - - + -
609B VAL* 4.2 24.5 - - + -
611B LEU* 4.7 11.2 - - + -
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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