Contacts of the helix formed by residues 57 - 61 (chain L) in PDB entry 1KYO
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 GLY 57 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L SER* 1.3 75.8 - - - +
58L ALA* 1.3 66.6 + - - +
59L ALA 3.1 2.7 - - - -
60L ASN* 2.7 28.7 + - - +
61L GLU* 3.5 8.0 - - - +
69L SER* 4.3 8.1 - - - -
96L ILE* 5.6 0.2 - - - -
97L SER 3.7 6.5 - - - -
98L ARG 3.5 8.0 + - - -
99L ASP 4.1 0.2 + - - -
100L PHE 3.7 5.4 - - - -
101L GLN* 3.9 9.9 - - - -
195L PHE* 4.3 2.5 - - - -
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Residues in contact with ALA 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L GLY* 1.3 71.0 - - - -
59L ALA* 1.3 60.8 - - - +
60L ASN 3.1 1.6 + - - -
61L GLU* 3.2 32.2 + - - +
69L SER* 4.7 0.6 + - - -
96L ILE* 4.9 4.2 - - + +
97L SER 3.0 18.2 + - - +
98L ARG* 3.8 9.0 - - - -
175L LEU* 3.7 26.2 - - + +
176L PRO 4.6 2.0 - - - +
177L THR* 3.8 31.4 - - + +
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Residues in contact with ALA 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L ALA* 1.3 76.9 - - - +
60L ASN* 1.3 61.7 + - - +
61L GLU 3.4 4.7 + - - +
98L ARG* 3.0 23.4 + - + +
99L ASP* 4.8 4.3 - - - +
172L PRO* 3.4 27.2 - - + +
173L LEU* 4.0 25.4 - - + +
175L LEU* 5.2 0.4 - - - -
238L LYS* 3.1 25.0 + - - +
323L ASP* 5.9 1.1 - - - +
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Residues in contact with ASN 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L GLY 4.5 2.6 + - - +
56L SER* 3.3 19.9 + - - +
57L GLY* 2.7 37.9 + - - +
59L ALA* 1.3 81.4 - - - +
61L GLU* 1.3 63.6 + - - +
62L ASN* 5.0 3.5 + - - +
98L ARG 4.0 5.1 + - - -
99L ASP* 4.5 2.6 + - - +
195L PHE* 4.1 5.6 - - + -
199L HIS* 4.0 30.7 + - + +
236L VAL 5.5 1.6 - - - +
238L LYS* 4.0 26.7 + - + +
322L LYS* 5.7 2.6 + - - -
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Residues in contact with GLU 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L GLY 3.5 8.1 - - - +
58L ALA* 3.2 24.2 + - - +
59L ALA 4.3 2.8 - - - +
60L ASN* 1.3 82.8 - - - +
62L ASN* 1.3 68.9 + - - +
63L PRO* 4.9 0.2 - - - +
65L ASN* 3.5 11.9 - - - +
66L ASN* 2.9 15.3 - - - +
67L GLY* 2.7 29.3 + - - -
68L VAL* 3.5 18.6 - - + +
69L SER* 2.8 37.8 + - - -
70L ASN 4.7 0.3 + - - -
172L PRO* 5.8 0.2 - - - +
175L LEU* 3.9 16.1 - - + +
177L THR 5.3 2.4 - - - +
195L PHE* 4.1 5.6 - - + -
238L LYS* 5.9 0.9 - - - +
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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