Contacts of the helix formed by residues 359 - 367 (chain C) in PDB entry 3KYS
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 GLU 359 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C LEU* 4.2 1.6 - - - +
358C PRO* 1.3 87.1 - - + +
360C LYS* 1.3 65.8 + - - +
361C TYR* 3.3 38.0 - - + +
362C MET* 3.1 24.8 + - + +
363C MET* 3.4 17.2 + - - +
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Residues in contact with LYS 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C LEU* 6.5 0.2 - - - -
280C ASN* 6.0 4.6 - - - +
359C GLU* 1.3 73.3 + - - +
361C TYR* 1.3 60.7 + - - +
363C MET* 2.9 20.2 + - + +
364C ASN* 2.8 36.4 + - - +
394C VAL* 4.1 22.2 - - + +
395C SER 3.3 27.0 + - - +
396C ASN* 3.9 31.9 + - + +
397C SER 4.8 3.2 + - - -
398C GLU* 6.0 2.4 - - - +
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Residues in contact with TYR 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C GLU* 3.4 41.3 - - + +
360C LYS* 1.3 78.0 - - - +
362C MET* 1.3 85.3 + - + +
364C ASN* 3.5 11.5 + - - +
365C SER* 2.9 33.6 + - - -
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Residues in contact with MET 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C LEU* 4.1 9.4 - - + -
358C PRO* 3.4 27.6 - - + -
359C GLU* 3.1 49.7 + - + +
360C LYS 3.1 0.4 - - - -
361C TYR* 1.3 101.7 - - + +
363C MET* 1.3 64.8 + - - +
365C SER* 3.0 16.9 + - - -
366C VAL* 3.0 19.2 + - - +
72D VAL* 4.7 3.1 - - + +
73D MET* 4.0 32.3 - - + +
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Residues in contact with MET 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C LEU* 3.5 35.9 - - + -
354C LEU* 3.4 40.2 - - + +
355C LYS* 4.8 5.4 - - + +
357C LEU* 3.8 18.3 - - + +
359C GLU 3.4 15.0 + - - +
360C LYS* 2.9 22.7 + - + +
362C MET* 1.3 79.0 - - - +
364C ASN* 1.3 62.7 + - - +
366C VAL* 3.2 4.9 + - - +
367C LEU* 3.1 26.0 + - - +
394C VAL* 3.7 28.7 - - + -
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Residues in contact with ASN 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C LYS* 2.8 25.7 + - - +
361C TYR* 3.7 9.4 - - - +
363C MET* 1.3 72.1 - - - +
365C SER* 1.3 62.7 + - - +
367C LEU* 3.5 8.0 + - - +
368C GLU* 3.3 21.5 + - - +
393C GLU* 3.2 29.3 - - + +
394C VAL* 2.5 45.6 + - - +
396C ASN* 6.3 1.0 - - - +
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Residues in contact with SER 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C TYR* 2.9 23.0 + - - -
362C MET* 3.0 10.8 + - - -
364C ASN* 1.3 75.2 - - - +
366C VAL* 1.3 64.8 + - - +
368C GLU* 3.2 25.4 + - - +
369C ASN* 4.6 2.1 - - - +
72D VAL* 3.6 30.9 - - - +
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Residues in contact with VAL 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C PHE* 4.3 7.6 - - + -
354C LEU* 3.4 25.6 - - + -
357C LEU* 4.1 11.9 - - + -
362C MET 3.0 14.1 + - - +
363C MET* 3.3 10.1 - - - +
365C SER* 1.3 76.3 - - - +
367C LEU* 1.3 66.7 + - - +
368C GLU 3.1 1.3 + - - -
369C ASN* 3.3 17.5 + - - +
370C PHE* 4.1 2.9 + - - +
68D LEU* 4.0 25.8 - - + +
69D PHE* 4.2 22.7 - - + +
72D VAL* 3.8 27.4 - - + -
73D MET* 5.0 2.7 - - + -
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Residues in contact with LEU 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LYS* 5.6 0.3 - - - -
277C ALA* 6.1 1.6 - - + -
344C P1L 4.2 8.3 - - + -
350C PHE* 3.6 32.1 - - + -
354C LEU* 4.2 8.5 - - + -
363C MET 3.1 12.1 + - - +
364C ASN* 3.7 6.1 - - - +
365C SER 3.3 0.2 - - - -
366C VAL* 1.3 77.6 - - - +
368C GLU* 1.3 64.6 + - - +
369C ASN 3.1 2.9 - - - -
370C PHE* 3.2 35.9 + - + +
391C VAL* 5.9 1.6 - - - +
392C PHE* 3.4 41.0 + - + +
393C GLU* 4.0 1.1 - - - -
394C VAL* 3.6 40.6 - - + +
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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