Contacts of the strand formed by residues 110 - 115 (chain C) in PDB entry 1KI1
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 PHE 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C VAL* 4.7 1.6 - - - -
78C PHE* 3.3 27.1 - - + +
80C VAL* 3.8 12.1 - - + -
98C VAL* 3.9 33.7 - - + -
101C ILE* 3.9 17.7 - - + -
102C THR* 5.2 3.4 - - - -
108C THR 4.5 5.6 - - - -
109C PRO* 1.3 78.6 - - + +
111C LEU* 1.3 77.0 + - - +
112C LEU* 4.7 6.3 - - + -
149C LEU* 3.5 25.8 - - + -
150C LYS 3.6 15.0 - - - -
151C ALA* 3.3 23.3 - - + -
152C VAL* 2.9 27.2 + - - +
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Residues in contact with LEU 111 (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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77C VAL* 5.0 2.5 - - + -
78C PHE 3.0 6.4 + - - +
79C LEU* 3.7 26.1 - - + -
80C VAL* 3.0 29.8 + - - +
110C PHE* 1.3 79.5 - - - +
112C LEU* 1.3 62.0 + - - +
113C VAL* 3.7 4.7 + - + -
152C VAL* 3.8 26.2 - - + -
153C LYS* 3.6 23.6 - - + +
155C VAL* 4.4 13.0 - - + -
168C VAL 3.8 8.5 - - - +
171C GLU* 3.8 9.9 - - + +
172C ALA* 3.6 27.8 - - - +
175C ALA* 4.1 14.6 - - + -
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Residues in contact with LEU 112 (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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80C VAL* 3.6 9.9 - - + +
82C PHE* 3.3 36.8 - - + -
90C PHE* 4.7 0.4 - - + -
93C VAL* 4.2 20.4 - - + -
110C PHE* 4.9 5.2 - - + -
111C LEU* 1.3 71.6 - - - +
113C VAL* 1.3 59.6 + - - +
142C ALA* 3.5 26.2 - - - +
145C LEU* 4.3 15.9 - - + +
146C ALA* 3.8 17.7 - - + +
149C LEU* 5.6 1.8 - - + -
151C ALA* 4.2 10.8 - - + +
153C LYS 3.0 13.6 + - - +
154C TYR* 3.3 12.8 - - + -
155C VAL* 3.1 26.7 + - - +
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Residues in contact with VAL 113 (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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19C LEU* 5.0 3.8 - - + -
79C LEU* 3.9 36.6 - - + -
80C VAL 2.7 15.1 + - - +
81C CYS* 3.3 18.0 - - - +
82C PHE* 3.1 29.8 + - - -
111C LEU* 4.1 5.6 - - + +
112C LEU* 1.3 75.6 - - - +
114C GLY* 1.3 72.2 + - - +
115C THR* 4.7 2.5 - - - +
155C VAL* 3.5 22.9 - - + +
157C CYS* 4.3 13.2 - - - -
168C VAL* 4.2 13.0 - - + -
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Residues in contact with GLY 114 (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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82C PHE* 3.6 9.9 - - - -
84C VAL* 3.8 6.1 - - - -
113C VAL* 1.3 77.3 - - - +
115C THR* 1.3 60.9 + - - -
117C ILE* 4.7 0.2 - - - -
154C TYR* 3.3 29.4 - - - -
155C VAL 2.7 13.4 + - - -
156C GLU* 3.3 3.6 - - - -
157C CYS* 3.1 25.6 + - - -
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Residues in contact with THR 115 (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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14C VAL* 2.5 31.0 + - - +
15C GLY* 4.8 0.8 + - - -
19C LEU* 3.7 24.1 - - - +
81C CYS* 4.6 5.6 - - - +
82C PHE 2.8 17.0 + - - -
83C SER* 3.3 14.1 - - - +
84C VAL* 2.8 26.8 + - - +
113C VAL* 4.5 2.8 + - - +
114C GLY* 1.3 75.1 + - - -
116C GLN* 1.3 83.6 + - + +
117C ILE 3.3 3.1 - - - -
157C CYS* 3.8 6.1 - - - -
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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