Contacts of the helix formed by residues 111 - 123 (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 SER 111 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88L GLU 5.4 2.4 + - - -
89L GLY 5.5 1.6 - - - -
90L LEU* 5.0 2.7 - - - -
107L SER* 4.0 10.7 + - - -
108L LEU* 3.2 25.8 + - - +
110L GLY* 1.3 71.1 - - - +
112L THR* 1.3 52.4 + - - +
113L ASP* 3.0 6.7 - - - +
114L LYS* 2.8 51.8 + - - +
115L SER* 3.4 7.8 + - - -
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Residues in contact with THR 112 (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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50L VAL* 4.6 11.0 - - - +
107L SER* 4.5 8.3 - - - -
108L LEU 3.8 0.8 + - - -
109L PRO 3.6 8.8 + - - +
110L GLY* 2.8 13.7 + - - +
111L SER* 1.3 75.6 - - - +
113L ASP* 1.3 69.1 + - + +
115L SER* 4.0 12.5 - - - -
116L LEU* 4.1 13.3 + - - +
213L ILE* 3.4 37.5 - - + +
217L ASP* 4.6 19.1 - - + +
218L LEU* 4.9 6.4 - - - +
221L SER* 5.9 0.2 - - - +
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Residues in contact with ASP 113 (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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110L GLY 4.3 2.2 + - - +
111L SER 3.0 0.8 - - - -
112L THR* 1.3 85.3 - - + +
114L LYS* 1.3 70.6 + - - +
115L SER 3.1 2.7 + - - -
116L LEU* 3.5 5.8 + - - +
117L ASP* 3.3 34.0 + - - +
221L SER* 2.9 31.0 + - - -
225L LYS* 4.4 14.6 + - - -
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Residues in contact with LYS 114 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88L GLU* 3.1 49.6 + - + +
90L LEU* 3.9 15.5 - - + +
111L SER* 2.8 32.1 + - - +
113L ASP* 1.3 84.0 - - - +
115L SER* 1.3 60.4 - - - +
117L ASP* 3.7 13.9 + - - +
118L PHE* 3.6 17.5 + - - +
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Residues in contact with SER 115 (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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50L VAL* 4.5 20.4 - - - +
90L LEU* 4.4 1.9 - - - +
105L VAL* 3.9 27.2 + - - +
107L SER* 2.9 31.7 + - - -
111L SER 3.4 1.1 + - - -
112L THR 4.0 10.7 + - - -
113L ASP 3.1 0.2 - - - -
114L LYS* 1.3 75.2 - - - +
116L LEU* 1.3 57.7 + - - +
117L ASP 3.1 1.3 - - - -
118L PHE* 2.7 26.7 + - - +
119L LEU* 2.9 17.1 + - - +
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Residues in contact with LEU 116 (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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50L VAL* 4.0 22.9 - - + -
112L THR 4.1 10.5 + - - +
113L ASP* 3.5 9.6 + - - +
115L SER* 1.3 78.3 - - - +
117L ASP* 1.3 57.3 + - - +
118L PHE 3.1 0.2 - - - -
119L LEU* 3.7 11.6 - - + +
120L ASN* 3.0 33.1 + - - +
207L VAL* 4.8 6.3 - - + -
218L LEU* 3.6 23.8 - - + -
221L SER* 3.7 30.5 - - - +
222L ILE* 4.0 23.8 - - + -
225L LYS* 4.8 10.3 - - - +
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Residues in contact with ASP 117 (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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113L ASP* 3.3 24.9 + - - +
114L LYS* 4.0 16.1 + - - +
115L SER 3.1 1.0 - - - -
116L LEU* 1.3 77.3 - - - +
118L PHE* 1.3 56.7 - - - +
120L ASN* 4.8 3.0 - - - +
121L GLN* 3.2 24.0 + - - +
225L LYS* 3.3 29.7 + - - -
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Residues in contact with PHE 118 (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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76L PHE* 4.6 6.3 - + - -
81L ASN* 3.5 39.9 - - - -
84L VAL* 3.7 26.0 - - + -
85L ALA* 3.5 23.8 - - + -
88L GLU* 6.0 0.9 - - + -
90L LEU* 4.1 13.5 - - + -
92L LEU* 3.4 22.4 - - + -
105L VAL* 4.0 17.0 - - + -
114L LYS 3.6 9.8 + - - +
115L SER* 2.7 10.5 + - - +
117L ASP* 1.3 79.0 - - - +
119L LEU* 1.3 66.5 - - - +
120L ASN 3.2 1.1 - - - -
121L GLN* 3.2 14.8 + - - +
122L SER* 3.0 33.7 + - - -
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Residues in contact with LEU 119 (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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50L VAL* 3.6 21.1 - - + +
51L GLY* 4.4 4.7 - - - -
52L VAL* 3.6 39.3 - - + +
76L PHE* 5.3 2.2 - - + -
103L TYR* 4.2 4.9 - - + +
105L VAL* 3.4 32.8 - - + +
115L SER* 2.9 14.4 + - - +
116L LEU* 3.7 20.4 - - + +
118L PHE* 1.3 80.8 - - - +
120L ASN* 1.3 57.0 + - + +
122L SER* 3.2 1.5 + - - -
123L PHE* 3.0 45.6 + - + +
207L VAL* 5.9 2.2 - - + -
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Residues in contact with ASN 120 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116L LEU 3.0 16.2 + - - +
117L ASP* 4.8 3.6 - - - +
119L LEU* 1.3 78.4 - - - +
121L GLN* 1.3 63.7 + - - +
123L PHE* 4.5 4.3 - - - +
124L ILE* 3.1 56.4 + - - +
125L GLN 3.7 0.3 + - - -
225L LYS* 5.9 11.2 - - + +
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Residues in contact with GLN 121 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84L VAL* 3.8 24.8 - - - +
117L ASP 3.2 20.8 + - - +
118L PHE* 3.2 15.9 + - - +
120L ASN* 1.3 79.3 - - - +
122L SER* 1.3 53.0 + - - +
125L GLN* 3.2 40.9 + - + +
126L GLN* 2.6 46.3 + - - +
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Residues in contact with SER 122 (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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76L PHE* 4.6 13.9 - - - -
81L ASN* 3.1 34.4 + - - -
118L PHE* 3.0 26.7 + - - -
119L LEU 3.9 2.5 - - - -
121L GLN* 1.3 78.3 - - - +
123L PHE* 1.3 58.9 + - - +
124L ILE 3.5 0.7 - - - -
126L GLN* 3.9 21.2 + - - +
127L LYS* 3.4 23.7 + - - +
130L LEU* 4.7 5.6 - - - +
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Residues in contact with PHE 123 (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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52L VAL* 3.6 18.8 - - + -
54L PHE* 3.6 27.6 - + - -
72L TRP* 6.0 0.4 - + - -
76L PHE* 3.7 26.7 - + - -
103L TYR* 3.4 34.1 - + + -
119L LEU* 3.0 34.7 + - + +
120L ASN* 3.8 2.9 - - - +
122L SER* 1.3 78.8 - - - +
124L ILE* 1.3 69.7 + - + +
127L LYS* 3.3 39.6 - - - +
200L PHE* 4.3 11.0 - + + -
229L LEU* 4.8 8.5 - - - +
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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