Contacts of the helix formed by residues 555 - 563 (chain A) in PDB entry 5CHG
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 THR 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A TYR* 6.1 0.7 - - - +
500A ALA* 3.6 11.2 - - - +
553A THR 4.3 0.5 - - - -
554A PRO* 1.3 86.8 - - + +
556A GLU* 1.3 66.0 + - - +
557A LYS* 3.6 21.2 + - + +
558A ASP* 3.0 37.0 + - - +
559A VAL* 3.7 3.8 + - - +
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Residues in contact with GLU 556 (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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419A ARG* 2.5 38.3 + - - -
500A ALA* 3.8 20.1 - - - +
503A LEU* 4.3 12.4 - - + +
504A LEU* 3.5 23.4 + - + +
555A THR* 1.3 72.7 - - - +
557A LYS* 1.3 58.2 + - + +
559A VAL* 2.9 26.9 + - - +
560A PHE* 3.3 14.6 + - - -
567A TYR* 4.1 11.2 + - + +
573A ARG* 2.6 42.5 + - - +
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Residues in contact with LYS 557 (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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555A THR* 3.2 15.9 - - - +
556A GLU* 1.3 77.7 - - + +
558A ASP* 1.3 63.2 + - - +
560A PHE* 3.5 3.3 + - - +
561A ARG* 3.1 23.1 + - - +
567A TYR* 3.6 55.2 - - + +
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Residues in contact with ASP 558 (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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552A PRO 5.1 0.2 - - - +
553A THR* 4.3 14.6 - - + -
554A PRO* 3.2 18.2 - - + +
555A THR* 3.0 37.7 + - - +
556A GLU 3.1 0.2 + - - -
557A LYS* 1.3 76.9 - - - +
559A VAL* 1.3 65.8 + - - +
561A ARG* 3.2 32.5 + - - +
562A LEU* 3.0 32.3 + - + +
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Residues in contact with VAL 559 (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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500A ALA* 4.5 4.3 - - + -
501A CYS* 4.4 11.7 - - - +
504A LEU* 3.8 28.0 - - + -
516A MET* 4.1 7.9 - - + -
527A LEU* 4.3 12.3 - - + -
532A LEU* 4.2 17.9 - - + +
553A THR* 3.7 28.7 - - + +
555A THR 3.9 5.4 - - - +
556A GLU* 2.9 14.7 + - - +
558A ASP* 1.3 77.2 - - - +
560A PHE* 1.3 63.2 + - - +
562A LEU* 3.4 1.6 + - - +
563A LEU* 3.3 31.5 + - + +
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Residues in contact with PHE 560 (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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504A LEU* 4.1 19.3 - - + -
512A PHE* 3.5 32.5 - + - -
516A MET* 3.7 22.4 - - + -
556A GLU 3.3 10.5 + - - -
557A LYS 3.7 7.2 - - - +
559A VAL* 1.3 77.9 - - - +
561A ARG* 1.3 61.4 - - - +
563A LEU* 3.3 6.2 + - - -
565A LEU* 3.0 52.4 + - + +
566A PRO 3.8 15.9 - - - -
567A TYR* 3.4 35.2 - + + -
568A ARG* 3.8 28.9 - - + -
573A ARG* 4.1 6.1 - - - -
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Residues in contact with ARG 561 (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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552A PRO 5.6 1.8 + - - -
554A PRO* 6.0 0.2 - - - +
557A LYS 3.1 15.1 + - - +
558A ASP* 3.2 40.7 + - - +
560A PHE* 1.3 74.4 - - - +
562A LEU* 1.3 86.1 + - + +
563A LEU 3.1 4.5 - - - -
564A GLY* 3.1 18.4 + - - -
565A LEU 4.5 4.5 - - - +
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Residues in contact with LEU 562 (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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523A LYS* 5.3 0.7 - - - +
525A MET* 3.5 20.1 - - + +
532A LEU* 3.8 19.3 - - + -
551A LEU* 4.2 26.0 - - + -
552A PRO 4.5 6.1 - - - +
553A THR* 3.9 24.5 - - + -
558A ASP* 3.0 21.9 + - + +
559A VAL 3.4 0.4 + - - +
561A ARG* 1.3 105.7 - - + +
563A LEU* 1.3 60.0 + - - +
564A GLY 3.4 0.8 + - - -
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Residues in contact with LEU 563 (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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516A MET* 3.8 37.2 - - + +
519A LEU* 4.2 3.6 - - + +
520A ALA* 3.6 34.1 - - + +
523A LYS* 3.1 29.8 - - + -
525A MET* 3.8 25.1 - - + -
527A LEU* 4.5 7.2 - - + -
532A LEU* 4.0 8.5 - - + -
559A VAL* 3.3 25.6 + - + +
560A PHE 3.8 4.9 - - - +
561A ARG 3.1 1.2 - - - -
562A LEU* 1.3 77.8 - - - +
564A GLY* 1.3 64.6 + - - +
565A LEU* 3.7 16.4 - - + +
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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