Contacts of the helix formed by residues 115 - 131 (chain B) in PDB entry 1KCX
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 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PRO* 4.7 0.8 - - - +
114B SER* 1.3 76.8 + - - +
116B LEU* 1.3 62.8 + - - +
117B LEU* 3.3 3.5 + - - +
118B THR* 3.1 33.8 + - - -
119B SER* 3.2 23.0 + - - -
145B TYR* 5.4 0.2 - - - -
151B GLU* 2.6 31.2 + - - -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 5.2 0.2 - - - +
110B PRO* 3.8 29.0 - - + +
114B SER 3.6 0.6 + - - -
115B SER* 1.3 72.5 - - - +
117B LEU* 1.3 58.2 + - - +
119B SER* 3.3 3.1 + - - -
120B PHE* 2.9 29.2 + - - +
139B VAL* 4.1 15.6 - - + +
140B ASP 4.2 6.1 - - - +
141B ILE* 4.7 11.4 - - + -
142B THR* 5.4 1.3 - - - +
143B SER 5.9 0.2 - - - +
145B TYR* 3.3 24.3 + - + +
148B VAL* 3.7 19.5 - - + +
151B GLU* 3.1 11.1 + - + +
152B LEU* 3.4 34.3 - - + -
155B LEU* 3.8 19.8 - - + +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 3.6 2.2 - - - +
116B LEU* 1.3 79.2 - - - +
118B THR* 1.3 57.6 + - - +
120B PHE* 3.3 7.2 + - + +
121B GLU* 3.0 29.3 + - - +
151B GLU* 2.9 36.8 + - + +
154B VAL* 3.9 32.8 - - + -
155B LEU* 3.8 26.9 - - + -
159B LYS* 4.4 15.0 - - - -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER* 6.3 0.4 - - - -
115B SER* 3.1 28.9 + - - -
116B LEU 3.3 0.2 - - - -
117B LEU* 1.3 76.0 - - - +
119B SER* 1.3 62.5 + - - +
121B GLU* 3.3 23.9 + - - +
122B LYS* 3.1 21.7 + - + +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 3.6 19.1 - - - -
109B VAL 4.4 1.2 + - - -
110B PRO* 3.4 30.8 - - - +
111B GLU* 4.3 7.4 + - - +
114B SER* 4.7 2.6 + - - -
115B SER 3.2 10.7 + - - -
116B LEU 3.8 6.1 - - - -
118B THR* 1.3 75.0 - - - +
120B PHE* 1.3 66.1 + - - +
122B LYS* 3.2 9.3 + - - +
123B TRP* 3.0 37.2 + - - +
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 3.9 10.3 - - + +
116B LEU 2.9 14.2 + - - +
117B LEU* 3.4 10.3 - - + +
119B SER* 1.3 76.8 - - - +
121B GLU* 1.3 58.9 + - + +
123B TRP* 3.7 1.7 - - - +
124B HIS* 2.8 54.3 + + + +
137B LEU* 3.7 28.9 - - + -
139B VAL* 4.6 9.0 - - + -
155B LEU* 3.7 25.8 - - + -
159B LYS* 3.8 44.2 - - + -
161B VAL* 3.6 21.1 - - + -
468B PHE* 4.2 12.3 - + - -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU 3.0 12.8 + - - +
118B THR* 3.4 28.6 + - - +
120B PHE* 1.3 84.5 - - + +
122B LYS* 1.3 58.1 + - + +
124B HIS* 3.4 6.6 + - - +
125B GLU* 3.0 32.6 + - + +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN* 4.9 9.4 - - - +
111B GLU* 5.5 10.7 + - - +
118B THR* 3.1 13.7 + - + +
119B SER* 3.2 11.4 + - - +
121B GLU* 1.3 76.6 - - + +
123B TRP* 1.3 95.6 + - - +
125B GLU* 3.4 13.3 + - - +
126B ALA* 3.2 23.6 + - - +
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Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN* 3.1 45.5 - - + +
79B PRO* 4.5 3.8 - - + -
89B PHE* 3.9 21.1 - + - -
106B ASP* 3.3 25.7 + - - -
107B HIS 3.4 7.2 + - - -
108B VAL* 3.4 38.8 - - + -
109B VAL* 3.4 42.2 - - + -
119B SER* 3.0 29.8 + - - +
120B PHE 3.7 1.1 - - - +
122B LYS* 1.3 106.7 - - - +
124B HIS* 1.3 63.4 + - - +
126B ALA* 3.4 5.3 + - - +
127B ALA* 3.0 25.7 + - - +
137B LEU* 4.6 6.7 - - + -
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Residues in contact with HIS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 2.8 34.8 + + + +
121B GLU* 3.7 7.4 - - - +
123B TRP* 1.3 78.8 - - - +
125B GLU* 1.3 63.5 + - - +
127B ALA* 3.5 2.2 + - - -
128B ASP* 2.7 48.9 + - - +
135B TYR* 3.5 7.3 + - - -
137B LEU* 4.2 12.5 - - + +
468B PHE* 3.6 39.0 - + + +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLU* 3.0 21.4 + - + +
122B LYS* 3.7 12.2 - - - +
124B HIS* 1.3 80.2 - - - +
126B ALA* 1.3 59.2 + - - +
128B ASP* 3.7 3.9 + - - +
129B THR* 3.1 40.6 + - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN* 3.0 34.5 - - - +
89B PHE* 4.1 2.5 - - + -
122B LYS 3.2 14.6 + - - +
123B TRP 3.8 1.8 - - - +
124B HIS 3.3 0.2 - - - -
125B GLU* 1.3 77.8 - - - +
127B ALA* 1.3 59.6 + - - +
129B THR* 2.7 21.7 + - - -
130B LYS* 2.9 23.8 + - + +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.6 33.6 - - + -
123B TRP 3.0 16.8 + - - +
124B HIS 4.0 0.7 - - - +
126B ALA* 1.3 77.8 - - - +
128B ASP* 1.3 58.8 + - - +
131B SER* 2.7 33.2 + - - +
135B TYR* 3.4 36.7 - - + +
137B LEU* 5.3 0.2 - - + -
464B GLY* 4.8 0.2 - - - -
466B GLY 4.9 0.3 - - - +
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B HIS* 2.7 44.6 + - - +
125B GLU* 4.1 5.2 - - - +
127B ALA* 1.3 75.7 - - - +
129B THR* 1.3 61.1 + - + +
135B TYR* 2.6 24.4 + - - -
464B GLY* 3.5 20.7 - - - +
466B GLY 3.7 13.2 - - - +
467B ARG* 4.6 0.9 - - - -
468B PHE 4.0 6.6 + - - -
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLU* 3.1 23.9 + - + +
126B ALA* 2.7 23.7 + - - -
128B ASP* 1.3 81.9 - - + +
130B LYS* 1.3 67.4 + - - +
463B LYS* 3.2 21.8 + - - +
464B GLY* 3.4 13.6 + - - -
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN* 5.8 1.6 - - - +
88B ASP* 3.4 36.9 + - + +
89B PHE* 3.8 7.6 - - + -
90B PHE* 3.5 32.3 - - + +
126B ALA* 2.9 22.2 + - + +
129B THR* 1.3 87.9 - - - +
131B SER* 1.3 66.4 + - - +
132B CYS 3.5 1.6 + - - -
463B LYS* 3.6 23.0 - - + +
464B GLY 3.2 9.8 + - - +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.6 15.0 + - - +
93B THR* 3.5 14.4 - - - +
127B ALA* 2.7 31.9 + - - -
130B LYS* 1.3 71.9 - - - +
132B CYS* 1.3 59.0 + - - +
133B CYS* 2.7 28.8 + - - -
135B TYR* 3.8 16.2 - - - +
464B GLY* 3.0 19.4 + - - -
465B MET 3.0 0.3 + - - -
466B GLY* 3.0 17.8 + - - -
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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
------------------------------------------------------------
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