Contacts of the helix formed by residues 565 - 570 (chain B) in PDB entry 1KTA
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 SER 565 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561B LEU* 4.4 8.7 - - - +
562B HIS* 2.9 20.3 + - - -
563B PRO 3.3 1.6 - - - -
564B ALA* 1.3 77.4 - - - +
566B SER* 1.3 64.4 + - - +
567B SER* 2.8 25.9 + - - -
568B LEU* 3.0 17.0 + - - +
569B HIS* 3.2 9.7 - - - -
648B GLY 3.5 2.8 + - - -
649B ASN* 2.7 28.3 + - - -
650B GLU 3.5 9.0 - - - -
651B PRO* 4.7 0.7 - - - -
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Residues in contact with SER 566 (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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564B ALA 3.1 5.4 + - - -
565B SER* 1.3 71.6 + - - +
567B SER* 1.3 59.6 + - - +
568B LEU 3.2 0.2 - - - -
569B HIS* 4.0 2.7 - - - +
570B TYR* 3.1 36.3 + - - +
572B LEU* 3.5 35.6 + - - +
648B GLY* 3.5 2.8 - - - -
649B ASN 3.4 8.5 + - - -
650B GLU* 3.2 30.0 + - - +
652B SER 4.9 4.5 - - - -
654B GLY 5.7 1.8 - - - -
656B SER 5.5 1.6 - - - -
658B PRO* 4.0 4.7 - - - +
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Residues in contact with SER 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.7 14.0 - - - +
73A GLN* 2.9 18.0 + - - +
561B LEU* 4.0 4.9 - - - +
565B SER* 2.8 22.2 + - - -
566B SER* 1.3 76.9 - - - +
568B LEU* 1.3 66.9 + - - +
571B SER* 3.9 2.8 - - - -
572B LEU 3.7 11.9 - - - +
573B GLN* 3.2 12.5 - - - +
647B ILE* 3.7 22.4 - - - +
648B GLY 3.1 21.6 + - - -
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Residues in contact with LEU 568 (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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59A LEU* 3.8 29.2 - - + -
61A LEU* 4.3 5.8 - - + -
67A SER* 3.7 28.5 - - - +
68A LEU* 3.6 25.1 - - + -
73A GLN* 3.1 31.0 + - - +
74A LEU 5.2 1.4 + - - +
75A PHE* 5.8 0.3 - - - +
145A VAL* 4.5 10.1 - - + +
147A ILE* 4.3 15.0 - - + -
164A PHE* 4.8 6.5 - - + -
561B LEU* 4.2 14.6 - - + -
562B HIS 4.9 1.1 - - - +
563B PRO 5.1 1.3 - - - +
565B SER* 3.0 15.6 + - - +
567B SER* 1.3 85.9 - - - +
569B HIS* 1.3 63.7 + - + +
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Residues in contact with HIS 569 (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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73A GLN* 3.6 2.9 - - - -
75A PHE* 3.3 16.0 - - + +
143A ARG* 2.9 36.3 + - + +
145A VAL* 3.5 29.5 - - + +
164A PHE* 4.5 1.4 - - - -
166A ILE* 4.4 2.9 - - + -
204A GLY* 3.2 15.9 - - - -
563B PRO 2.7 25.4 + - - -
564B ALA* 3.3 12.4 - - - +
565B SER 3.2 19.2 + - - +
566B SER* 4.9 0.9 - - - -
568B LEU* 1.3 84.4 - - + +
570B TYR* 1.3 93.1 + - + +
653B LEU* 3.7 11.9 - - + -
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Residues in contact with TYR 570 (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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75A PHE* 3.6 14.1 - + - -
143A ARG* 2.9 25.8 + - - -
204A GLY 3.4 6.7 - - - -
207A TYR* 3.7 24.7 - + + -
208A GLY* 2.8 32.5 + - - +
211A VAL* 5.9 1.1 - - + -
566B SER* 3.1 20.8 + - - +
569B HIS* 1.3 107.7 - - + +
571B SER* 1.3 59.5 + - - +
572B LEU* 3.2 11.9 + - + +
652B SER 4.5 2.5 - - - -
653B LEU* 2.5 38.2 + - - -
654B GLY 3.7 14.1 - - - -
655B VAL* 3.9 13.0 - - + -
656B SER 5.4 0.4 - - - -
3001B KIV 3.0 26.8 + - - -
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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