Contacts of the helix formed by residues 699 - 706 (chain A) in PDB entry 3KN5
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 MET 699 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A LEU 4.7 2.6 + - - +
617A SER 4.4 2.2 - - - +
651A GLU* 3.7 49.8 - - - +
652A ALA* 3.9 26.5 + - - +
697A PRO 5.6 1.1 - - - +
698A LEU* 1.3 76.1 - - - +
700A THR* 1.3 63.0 + - - +
701A PRO* 3.4 1.8 - - - -
702A ASP* 3.3 32.1 + - - +
703A ILE* 3.1 43.1 + - + +
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Residues in contact with THR 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ILE* 3.6 14.6 - - - +
516A PHE* 3.8 7.0 - - + -
614A THR 4.1 1.9 + - - -
615A MET* 2.9 28.4 + - - +
616A LEU 3.8 6.5 - - - +
617A SER 3.9 8.2 + - - -
618A GLY* 3.5 18.2 - - - +
698A LEU* 3.5 24.2 - - + -
699A MET* 1.3 73.7 - - - +
701A PRO* 1.3 68.9 - - + +
703A ILE 4.5 0.2 - - - +
704A LEU* 3.0 37.2 + - - +
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Residues in contact with PRO 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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510A ILE* 3.2 22.9 - - + +
511A LYS* 4.0 14.6 - - - +
513A LYS 3.1 26.7 - - - +
514A LYS* 4.6 6.5 - - - +
516A PHE* 3.5 30.3 - - + +
698A LEU 3.5 11.7 - - - +
699A MET 3.4 4.5 - - - -
700A THR* 1.3 97.8 - - + +
702A ASP* 1.3 57.3 + - + +
704A LEU* 4.1 0.4 - - + +
705A GLY* 3.2 20.6 + - - -
695B SER* 5.5 1.7 - - - +
696B ASN* 5.2 3.3 - - - +
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Residues in contact with ASP 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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699A MET* 3.3 36.5 + - - +
700A THR 3.2 0.4 - - - -
701A PRO* 1.3 80.9 - - + +
703A ILE* 1.3 66.1 + - - +
705A GLY* 3.3 2.2 + - - -
706A SER* 3.1 24.1 + - - -
695B SER* 4.3 13.4 + - - +
696B ASN* 6.1 0.2 - - - -
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Residues in contact with ILE 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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617A SER 3.2 22.9 - - - +
618A GLY 3.2 25.1 - - - +
619A GLN* 3.4 25.8 - - + +
651A GLU* 5.7 1.1 - - + +
652A ALA* 4.3 5.2 - - + -
699A MET* 3.1 42.1 + - + +
700A THR 4.0 2.5 - - - +
702A ASP* 1.3 75.3 - - - +
704A LEU* 1.3 64.1 + - - +
706A SER* 2.8 22.7 + - - +
707A SER* 3.7 8.1 + - - +
711A VAL* 5.4 2.7 - - + -
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Residues in contact with LEU 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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507A PHE* 4.1 40.2 - - + +
510A ILE* 4.5 7.9 - - + -
511A LYS* 3.3 23.2 - - + +
614A THR* 4.5 5.8 - - + +
618A GLY* 3.7 29.6 - - - +
700A THR* 3.0 32.8 + - - +
701A PRO 4.1 2.5 - - - +
703A ILE* 1.3 78.2 - - - +
705A GLY* 1.3 59.1 + - - +
707A SER 4.6 0.4 - - - -
708A GLY* 2.6 36.6 + - - -
711A VAL* 4.1 23.6 - - + -
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Residues in contact with GLY 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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511A LYS* 3.6 17.1 - - - +
701A PRO 3.2 11.5 + - - -
702A ASP 3.7 4.0 - - - -
703A ILE 3.2 0.8 - - - -
704A LEU* 1.3 75.9 - - - +
706A SER* 1.3 57.2 + - - +
707A SER* 2.9 11.6 + - - -
708A GLY 4.5 0.5 + - - -
515B HIS* 4.0 13.5 + - - -
695B SER* 3.5 26.5 + - - -
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Residues in contact with SER 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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702A ASP* 3.1 15.9 + - - -
703A ILE* 2.8 22.1 + - - +
705A GLY* 1.3 72.8 - - - +
707A SER* 1.3 63.8 + - - +
695B SER* 3.6 14.2 + - - -
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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