Contacts of the helix formed by residues 702 - 716 (chain H) in PDB entry 5KHU
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 702 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701H LYS* 3.7 30.1 - - - +
703H PRO* 3.8 28.7 - - - -
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Residues in contact with PRO 703 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702H ASN* 3.8 26.7 - - - -
704H LEU* 3.7 29.6 - - - -
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Residues in contact with LEU 704 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703H PRO* 3.7 29.6 - - - -
705H CYS* 3.8 26.7 - - - +
707H PHE* 4.3 16.2 - - - +
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Residues in contact with CYS 705 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704H LEU* 3.8 25.6 - - - +
706H LYS* 3.8 30.1 - - - +
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Residues in contact with LYS 706 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705H CYS* 3.8 29.2 - - - +
707H PHE* 3.8 25.1 - - - +
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Residues in contact with PHE 707 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704H LEU* 4.3 18.8 - - - +
706H LYS* 3.8 25.4 - - - +
708H HIS* 3.8 28.7 - - - +
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Residues in contact with HIS 708 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707H PHE* 3.8 29.4 - - - +
709H ARG* 3.8 27.1 - - - +
711H SER* 4.4 17.0 - - - +
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Residues in contact with ARG 709 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708H HIS* 3.8 26.2 - - - +
710H ALA* 3.8 29.8 - - - +
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Residues in contact with ALA 710 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709H ARG* 3.8 29.6 - - - +
711H SER* 3.8 26.2 - - - +
713H LEU* 4.3 16.6 - - - +
722H ALA* 4.2 24.9 - - - +
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Residues in contact with SER 711 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708H HIS* 4.4 17.3 - - - +
710H ALA* 3.8 28.7 - - - +
712H VAL* 3.8 24.5 - - - +
714H PHE* 4.6 13.7 - - - +
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Residues in contact with VAL 712 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711H SER* 3.8 25.8 - - - +
713H LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 713 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710H ALA* 4.3 16.4 - - - +
712H VAL* 3.8 29.4 - - - +
714H PHE* 3.8 24.5 - - - +
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Residues in contact with PHE 714 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711H SER* 4.6 17.3 - - - +
713H LEU* 3.8 25.4 - - - +
715H ALA* 3.8 29.2 - - - +
717H GLU* 4.3 16.6 - - - +
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Residues in contact with ALA 715 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714H PHE* 3.8 29.6 - - - +
716H ASN* 3.8 26.0 - - - +
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Residues in contact with ASN 716 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715H ALA* 3.8 28.9 - - - +
717H GLU* 3.8 26.5 - - - +
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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
------------------------------------------------------------
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