Contacts of the helix formed by residues 699 - 709 (chain A) in PDB entry 4K33
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 PRO 699 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A GLY 3.4 10.1 - - - +
698A ILE* 1.3 88.2 - - + +
700A VAL* 1.3 66.7 + - - +
701A GLU* 3.5 24.9 - - - +
702A GLU* 3.1 36.3 + - - +
703A LEU 3.1 15.6 + - - -
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Residues in contact with VAL 700 (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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658A VAL* 3.7 38.8 - - + +
659A LYS* 3.9 25.6 - - + -
698A ILE 3.4 1.2 + - - -
699A PRO* 1.3 72.2 - - - +
701A GLU* 1.3 74.1 + - + +
703A LEU* 3.0 23.4 + - - +
704A PHE* 3.4 6.6 + - - +
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Residues in contact with GLU 701 (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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699A PRO* 3.5 20.7 - - - +
700A VAL* 1.3 90.1 + - + +
702A GLU* 1.3 66.2 + - + +
704A PHE* 4.2 7.6 + - - +
705A LYS* 4.4 5.5 + - - +
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Residues in contact with GLU 702 (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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698A ILE* 4.6 5.3 - - + +
699A PRO* 3.1 42.0 + - + +
700A VAL 3.0 0.8 - - - -
701A GLU* 1.3 82.6 - - + +
703A LEU* 1.3 67.9 + - - +
704A PHE 2.9 2.9 - - - -
705A LYS* 2.9 25.4 + - + +
706A LEU* 3.0 22.3 + - + +
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Residues in contact with LEU 703 (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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658A VAL* 3.7 31.2 - - + +
659A LYS* 3.9 27.6 - - + +
666A LEU* 5.3 2.0 - - + -
695A TYR* 3.5 46.2 - - + -
698A ILE* 3.9 14.6 - - + +
699A PRO 3.1 12.3 + - - +
700A VAL* 3.0 12.5 + - - +
702A GLU* 1.3 75.4 - - - +
704A PHE* 1.3 61.7 + - + +
706A LEU* 3.4 6.4 + - + +
707A LEU* 2.9 42.7 + - + +
711A HIS* 5.5 0.4 - - + -
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Residues in contact with PHE 704 (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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663A PRO* 4.9 3.4 - - + -
666A LEU* 4.6 9.6 - - + -
667A PHE* 2.8 61.5 - + + -
700A VAL 3.4 7.2 + - - +
701A GLU 4.7 4.7 - - - +
702A GLU* 2.9 2.4 - - - +
703A LEU* 1.3 82.7 - - + +
705A LYS* 1.3 68.7 + - - +
706A LEU 3.1 0.2 + - - -
707A LEU* 3.3 11.7 + - + -
708A LYS* 3.1 61.8 + - + +
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Residues in contact with LYS 705 (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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701A GLU 4.4 3.7 + - - +
702A GLU* 2.9 22.2 + - - +
704A PHE* 1.3 75.8 - - - +
706A LEU* 1.3 73.6 + - - +
708A LYS* 3.2 16.0 - - + +
709A GLU* 3.0 64.4 + - + +
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Residues in contact with LEU 706 (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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698A ILE* 3.8 41.1 - - + -
702A GLU* 3.0 18.4 + - + +
703A LEU* 3.4 8.5 - - + +
705A LYS* 1.3 88.7 - - - +
707A LEU* 1.3 61.0 + - - +
709A GLU* 3.1 23.5 + - - +
711A HIS* 3.0 46.7 + - + +
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Residues in contact with LEU 707 (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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658A VAL 5.7 0.2 - - - +
661A MET 4.6 3.1 - - - +
663A PRO* 4.7 12.6 - - + +
666A LEU* 4.1 24.0 - - + -
678A TRP* 3.9 23.8 - - + -
695A TYR* 3.6 28.7 - - + +
703A LEU* 2.9 42.9 + - + +
704A PHE* 3.3 11.4 + - + +
706A LEU* 1.3 74.7 - - - +
708A LYS* 1.3 62.3 + - - +
710A GLY* 3.1 4.5 + - - -
711A HIS* 3.6 19.7 - - + +
712A ARG* 3.1 26.0 + - - +
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Residues in contact with LYS 708 (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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663A PRO* 6.3 0.9 - - - -
704A PHE* 3.1 56.1 + - + +
705A LYS* 3.2 17.3 + - + +
707A LEU* 1.3 77.2 - - - +
709A GLU* 1.3 61.7 + - + +
710A GLY* 3.0 4.1 + - - -
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Residues in contact with GLU 709 (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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705A LYS* 3.0 55.7 + - + +
706A LEU* 3.1 16.0 + - - +
708A LYS* 1.3 80.2 - - + +
710A GLY* 1.3 60.0 + - - +
711A HIS* 3.3 3.0 + - + +
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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