Contacts of the helix formed by residues 552 - 561 (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 TYR 552 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535B ILE* 3.4 34.1 - - + -
536B SER 3.6 17.3 - - - -
537B THR* 3.8 10.5 - - + -
538B ASP* 3.1 26.7 + - - +
551B SER* 1.3 73.8 - - - +
553B GLU* 1.3 80.3 + - + +
555B ARG* 3.3 13.8 + - - +
556B LYS* 2.9 57.6 + - + +
568B VAL* 4.8 0.7 - - - +
569B ILE 3.8 3.3 - - - -
570B PRO* 3.4 37.7 - - + +
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Residues in contact with GLU 553 (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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551B SER* 3.2 8.1 + - - +
552B TYR* 1.3 97.2 - - + +
554B HIS* 1.3 65.9 + - + +
556B LYS* 3.8 14.2 + - - +
557B LEU* 3.1 28.6 + - - +
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Residues in contact with HIS 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TRP* 3.3 69.5 + + + -
550B HIS* 4.5 8.0 - - + -
551B SER* 3.2 27.1 + - - +
553B GLU* 1.3 82.4 - - + +
555B ARG* 1.3 65.1 + - - +
557B LEU* 3.6 19.0 - - + +
558B ILE* 3.1 30.7 + - - +
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Residues in contact with ARG 555 (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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509B THR* 3.0 35.8 + - - +
510B PHE* 3.6 15.1 - - + +
511B ASP* 3.6 22.9 - - - +
535B ILE* 4.0 15.0 - - + +
536B SER 2.8 33.7 + - - +
537B THR 4.1 0.2 - - - -
538B ASP* 3.1 25.7 + - - -
541B ASN* 3.6 12.9 + - - -
548B ALA* 3.7 3.9 - - - +
550B HIS* 2.8 32.4 + - + +
551B SER 2.8 12.1 + - - +
552B TYR* 3.4 16.2 - - - +
554B HIS* 1.3 75.2 - - - +
556B LYS* 1.3 58.1 + - - +
558B ILE* 3.6 5.7 + - - +
559B LEU* 3.0 32.4 + - - +
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Residues in contact with LYS 556 (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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535B ILE* 3.6 15.8 - - + +
552B TYR* 2.9 48.5 + - + +
553B GLU* 3.8 17.4 + - - +
555B ARG* 1.3 74.1 - - - +
557B LEU* 1.3 59.7 + - - +
559B LEU* 3.1 3.0 + - - +
560B GLU* 2.9 66.2 + - - +
568B VAL* 3.8 27.3 + - + -
570B PRO* 6.1 0.4 - - - -
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Residues in contact with LEU 557 (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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15A TRP* 4.0 18.8 - - + +
18A ILE* 3.8 32.1 - - + -
19A LYS* 6.0 6.1 - - + -
553B GLU* 3.1 14.3 + - - +
554B HIS* 3.6 28.5 - - + +
556B LYS* 1.3 81.1 - - - +
558B ILE* 1.3 64.8 + - + +
560B GLU* 3.5 16.2 + - - +
561B THR* 3.3 20.3 + - + +
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Residues in contact with ILE 558 (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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13A LEU* 3.9 14.8 - - + +
14A HIS* 3.7 13.7 - - - +
15A TRP* 3.6 26.5 - - + +
18A ILE* 3.9 25.1 - - + -
513B LEU* 3.7 31.0 - - + -
550B HIS* 5.2 9.9 - - - +
554B HIS* 3.1 19.5 + - + +
555B ARG* 4.1 5.6 - - - +
557B LEU* 1.3 79.4 - - + +
559B LEU* 1.3 67.2 + - + +
561B THR* 3.0 23.0 + - - +
562B ILE* 3.7 6.9 - - + +
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Residues in contact with LEU 559 (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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510B PHE* 3.9 24.2 - - + +
513B LEU* 4.1 20.6 - - + -
521B LEU* 3.8 29.4 - - + -
533B VAL* 4.0 10.5 - - + -
535B ILE* 3.4 35.2 - - + -
555B ARG 3.0 20.7 + - - +
556B LYS 3.1 4.2 + - - +
558B ILE* 1.3 76.3 - - + +
560B GLU* 1.3 62.7 + - - +
561B THR 3.1 1.4 + - - -
562B ILE* 3.1 19.2 + - + +
565B VAL* 3.5 20.9 - - + +
568B VAL* 4.0 11.4 - - + -
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Residues in contact with GLU 560 (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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63A ARG* 3.1 21.7 + - - -
556B LYS* 2.9 55.0 + - - +
557B LEU* 3.8 14.4 - - - +
558B ILE 3.2 0.4 - - - -
559B LEU* 1.3 75.2 - - - +
561B THR* 1.3 58.6 + - + +
562B ILE 3.4 1.8 - - - -
565B VAL* 4.7 5.2 - - + +
567B GLU* 5.8 1.1 - - - -
568B VAL* 3.8 22.3 + - + +
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Residues in contact with THR 561 (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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18A ILE* 3.6 28.9 - - + +
62A ILE* 3.4 30.7 - - - +
63A ARG* 2.8 40.3 + - - +
64A TYR* 4.2 17.7 - - + +
557B LEU* 3.3 19.1 - - + +
558B ILE 3.0 12.9 + - - +
559B LEU 3.1 0.6 - - - -
560B GLU* 1.3 78.7 - - + +
562B ILE* 1.3 61.5 + - - +
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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