Contacts of the helix formed by residues 115 - 122 (chain M) 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 LYS 115 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G GLU* 3.0 32.8 + - - +
54M PHE* 4.2 3.3 - - - -
58M ASN* 5.7 3.1 - - + +
113M ALA* 4.1 18.5 - - + +
114M PHE* 1.3 79.7 - - - +
116M PRO* 1.3 78.7 - - + +
117M HIS* 3.2 17.0 - - + -
118M GLU* 3.0 45.6 + - + +
119M LEU* 3.5 4.0 + - - +
169M LEU* 4.3 1.1 - - - -
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Residues in contact with PRO 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M PHE 3.9 4.7 - - - +
115M LYS* 1.3 96.8 - - + +
117M HIS* 1.3 61.9 + - - +
119M LEU* 3.3 18.8 + - + +
120M THR* 3.5 11.1 + - - +
169M LEU* 3.6 26.6 - - + -
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Residues in contact with HIS 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ARG* 3.4 63.3 + - + +
109G GLU* 3.9 31.1 + - + -
58M ASN* 5.5 5.8 + - - -
115M LYS* 3.9 18.9 - - + +
116M PRO* 1.3 75.4 - - - +
118M GLU* 1.3 88.7 + - + +
119M LEU 3.1 2.0 - - - -
120M THR* 3.3 8.5 + - - +
121M GLU* 2.8 41.0 + - - +
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Residues in contact with GLU 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M PHE* 4.3 11.7 - - + -
57M GLN* 3.4 19.6 - - - +
58M ASN* 3.0 53.8 + - - +
64M ALA* 5.1 0.3 - - - +
114M PHE 4.0 6.8 + - - -
115M LYS* 3.0 33.8 + - + +
117M HIS* 1.3 96.9 - - + +
119M LEU* 1.3 56.9 - - - +
121M GLU* 4.9 0.4 - - - -
122M SER* 3.0 16.3 + - - +
123M VAL* 3.0 27.6 + - - +
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Residues in contact with LEU 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M LEU* 5.1 1.6 - - + -
54M PHE* 4.1 15.6 - - + -
115M LYS 3.5 3.1 + - - +
116M PRO* 3.3 13.4 + - + +
117M HIS 3.1 0.4 - - - -
118M GLU* 1.3 82.2 - - - +
120M THR* 1.3 65.5 + - + +
123M VAL* 3.4 14.3 + - + -
124M LEU* 2.8 58.5 + - + +
167M VAL 5.4 3.6 - - - +
168M SER 5.1 0.7 - - - -
169M LEU* 4.2 33.4 - - + +
172M ILE* 3.7 25.8 - - + -
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Residues in contact with THR 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M PRO 3.5 10.2 + - - +
117M HIS* 3.3 12.8 + - - +
119M LEU* 1.3 83.1 - - + +
121M GLU* 1.3 64.8 + - - +
124M LEU* 4.0 18.4 - - + +
125M PRO* 3.4 18.7 - - - +
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Residues in contact with GLU 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ARG* 3.1 33.9 + - - +
62G ARG* 2.8 39.6 + - - +
295L ARG* 4.2 12.1 + - - -
117M HIS* 2.8 28.3 + - + +
118M GLU* 4.9 0.4 - - - -
120M THR* 1.3 81.8 - - - +
122M SER* 1.3 62.5 + - - +
125M PRO* 3.6 11.9 - - - +
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Residues in contact with SER 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292L PRO* 4.0 14.8 - - - +
295L ARG* 5.1 6.3 + - - +
57M GLN* 3.5 31.3 + - - -
118M GLU* 3.0 14.3 + - - -
120M THR 3.7 0.2 - - - -
121M GLU* 1.3 85.4 + - - +
123M VAL* 1.3 69.7 + - - +
125M PRO* 3.4 4.3 - - - +
126M ALA* 3.2 23.6 + - - +
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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