Contacts of the helix formed by residues 365 - 370 (chain A) in PDB entry 5KZX
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 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A PRO* 1.3 93.5 - - + +
366A TYR* 1.3 67.2 + - - +
367A TRP* 3.4 44.9 - - + +
368A GLY* 3.0 14.4 + - - +
369A LEU* 4.0 3.1 + - - +
594A ARG* 3.8 19.2 - - + +
595A PRO 3.9 13.5 - - - +
596A PHE* 3.8 21.3 - - + -
710A TYR* 4.3 0.2 - - - -
862A GLY 3.2 13.0 - - - +
863A GLU* 4.4 7.0 - - + -
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Residues in contact with TYR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PRO 3.6 1.8 + - - -
365A PRO* 1.3 70.5 - - - +
367A TRP* 1.3 62.1 + - - +
369A LEU* 3.0 24.5 + - + +
370A GLY 4.0 1.7 + - - -
706A LEU* 3.3 20.9 - - + +
707A PRO* 3.3 29.3 - - - +
710A TYR* 3.4 53.0 - + + -
827A GLN* 3.7 9.0 + - - +
833A THR* 3.7 28.7 - - + +
836A SER* 4.5 4.3 + - - -
837A ARG* 3.2 50.3 - - + +
859A TRP* 3.8 13.6 - + - -
862A GLY* 2.9 17.0 + - - +
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Residues in contact with TRP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PRO* 3.4 28.7 - - + +
366A TYR* 1.3 78.4 - - - +
368A GLY* 1.3 59.3 + - - +
369A LEU 3.1 0.2 - - - -
370A GLY* 3.1 20.1 + - - -
399A ASP* 3.8 14.1 - - - +
400A VAL* 3.7 30.9 - - + +
437A ARG* 3.3 55.5 - - + +
439A MET* 4.8 1.8 - - + -
513A ASP* 3.6 40.8 - - + -
591A ARG* 4.4 9.6 - - - +
594A ARG 5.3 1.5 + - - -
596A PHE* 3.8 32.3 - + + -
833A THR* 3.5 23.7 + - - +
862A GLY 4.9 0.7 - - - -
863A GLU* 4.1 12.5 + - + +
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Residues in contact with GLY 368 (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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365A PRO 3.0 13.5 + - - -
367A TRP* 1.3 90.5 - - - +
369A LEU* 1.3 62.6 + - - +
370A GLY 3.4 0.4 - - - -
372A HIS* 2.7 23.7 + - - -
596A PHE* 3.7 31.3 - - - -
641A LEU* 4.8 1.2 - - - +
669A PRO 5.1 0.9 - - - +
670A PHE* 4.4 5.5 - - - -
671A MET 5.4 0.2 + - - -
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Residues in contact with LEU 369 (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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364A PRO* 4.2 11.4 - - + -
365A PRO 4.3 4.9 - - - +
366A TYR* 3.0 13.3 + - + +
368A GLY* 1.3 78.3 - - - +
370A GLY* 1.3 61.2 + - - +
641A LEU* 4.3 4.5 - - + -
669A PRO 3.8 10.5 - - - +
702A ARG* 2.9 32.2 + - - +
706A LEU* 3.5 22.7 - - + +
709A LEU* 4.0 9.9 - - + -
710A TYR* 3.9 47.8 - - + +
713A PHE* 3.4 37.7 - - + -
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TYR 4.0 1.4 + - - -
367A TRP 3.1 14.6 + - - -
368A GLY 3.9 0.2 - - - +
369A LEU* 1.3 82.7 - - - +
371A PHE* 1.3 62.3 + - - -
372A HIS* 3.1 20.8 - - - -
399A ASP* 3.9 8.5 - - - -
671A MET* 3.8 2.9 + - - +
702A ARG* 4.5 5.5 + - - -
703A TYR* 3.3 22.0 - - - -
706A LEU* 4.6 1.1 - - - -
833A THR* 4.5 4.1 - - - +
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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