Contacts of the helix formed by residues 122 - 135 (chain B) 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 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A PRO* 4.3 11.1 - - - +
295A ARG* 4.4 12.2 + - - +
57B GLN* 3.7 30.5 + - - -
118B GLU* 2.9 16.9 + - - -
120B THR 3.5 0.2 - - - -
121B GLU* 1.3 81.3 + - - +
123B VAL* 1.3 59.3 + - - +
125B PRO* 3.2 5.4 - - - +
126B ALA* 3.1 30.9 + - - +
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Residues in contact with VAL 123 (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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50B LEU* 3.7 39.5 - - + +
53B ARG* 3.9 20.6 - - + +
54B PHE* 3.7 35.0 - - + -
57B GLN* 4.4 8.5 - - + +
118B GLU 2.8 17.6 + - - +
119B LEU* 3.6 19.3 - - + +
122B SER* 1.3 69.2 - - - +
124B LEU* 1.3 61.5 + - - +
125B PRO 3.3 0.2 - - - -
126B ALA* 3.3 5.7 + - - +
127B ALA* 2.8 30.1 + - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 4.2 15.0 - - + -
119B LEU* 2.7 48.5 + - + +
120B THR* 4.1 17.9 - - + +
123B VAL* 1.3 72.0 - - - +
125B PRO* 1.4 66.4 - - + +
127B ALA* 3.2 4.6 + - - +
128B ARG* 2.8 42.5 + - - +
161B TYR* 4.2 27.1 - - + +
167B VAL 5.9 2.5 - - - +
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Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ARG* 5.4 5.4 - - - +
119B LEU 3.7 0.2 - - - +
120B THR 3.3 27.1 - - - +
121B GLU* 3.7 14.8 - - - +
122B SER 3.2 15.7 - - - +
124B LEU* 1.4 93.5 - - + +
126B ALA* 1.3 64.5 + - - +
127B ALA 2.9 0.3 + - - -
128B ARG* 2.9 13.6 + - + +
129B TYR* 3.0 13.1 + - - +
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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
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290A PHE 4.5 7.2 - - - +
292A PRO* 3.9 25.1 - - + -
53B ARG* 3.5 31.9 + - + +
122B SER 3.1 16.1 + - - +
123B VAL* 4.6 0.2 - - - -
125B PRO* 1.3 78.4 - - - +
127B ALA* 1.3 62.2 + - - +
129B TYR* 3.3 8.6 - - - +
130B ASP* 3.1 27.2 + - - +
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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
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49B HIS* 3.4 30.2 + - + +
50B LEU* 4.0 24.0 - - + -
53B ARG* 4.1 4.0 - - + +
123B VAL 2.8 17.6 + - - +
124B LEU* 3.6 4.7 - - - +
126B ALA* 1.3 73.2 - - - +
128B ARG* 1.3 59.3 + - - +
129B TYR 3.0 4.5 - - - -
130B ASP* 3.0 5.7 + - - +
131B TYR* 2.9 27.4 + - - +
161B TYR* 4.7 8.1 - - + -
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Residues in contact with ARG 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 LEU* 2.8 37.0 + - - +
125B PRO* 3.7 5.2 - - + +
127B ALA* 1.3 72.6 - - - +
129B TYR* 1.3 58.0 + - - +
131B TYR* 3.9 12.4 - - + +
132B ALA* 3.1 28.9 + - - +
161B TYR* 3.9 42.1 + - - -
162B ASP* 4.7 4.2 + - - +
163B GLY* 4.2 15.6 - - - +
234M ILE* 5.3 6.3 - - - +
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Residues in contact with TYR 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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288A ASN* 4.3 13.3 + - - -
290A PHE* 3.6 60.7 - + + +
291A GLU* 4.5 12.6 - - - -
53B ARG* 4.5 2.5 - - - -
125B PRO 3.0 10.7 + - - +
126B ALA* 3.3 13.0 - - - +
128B ARG* 1.3 74.4 - - - +
130B ASP* 1.3 88.1 + - - +
132B ALA* 2.9 17.7 + - + +
133B VAL* 3.0 38.3 + - + +
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Residues in contact with ASP 130 (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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291A GLU* 4.7 0.5 - - - +
49B HIS* 3.1 22.1 - - + +
53B ARG* 2.8 49.3 + - - -
126B ALA 3.1 4.1 + - - -
127B ALA 3.0 8.0 + - - +
129B TYR* 1.3 92.5 - - - +
131B TYR* 1.3 60.5 + - - +
133B VAL* 3.6 6.5 + - - +
134B ALA* 3.2 22.7 + - - +
160B LEU* 4.0 9.1 - - + +
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Residues in contact with TYR 131 (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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127B ALA 2.9 13.2 + - - +
128B ARG* 4.1 13.5 - - + +
130B ASP* 1.3 76.1 - - - +
132B ALA* 1.3 59.1 + - + +
134B ALA* 3.3 2.2 + - + +
135B GLU* 2.6 67.0 + - + +
160B LEU* 4.3 22.2 - - + +
161B TYR 3.6 25.1 - - - +
162B ASP* 3.7 30.5 + - + +
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Residues in contact with ALA 132 (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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128B ARG 3.1 18.7 + - - +
129B TYR* 2.9 6.5 + - + +
131B TYR* 1.3 76.2 - - + +
133B VAL* 1.3 67.0 + - + +
135B GLU* 3.5 31.5 + - - +
136B GLN* 3.6 16.5 + - - +
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Residues in contact with VAL 133 (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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129B TYR* 3.0 51.9 + - + +
130B ASP* 3.6 9.0 - - - +
132B ALA* 1.3 74.8 - - + +
134B ALA* 1.3 65.4 + - - +
136B GLN* 3.3 16.4 + - - +
137B CYS* 4.1 6.2 + - - +
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Residues in contact with ALA 134 (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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130B ASP 3.2 15.2 + - - +
131B TYR* 3.6 5.4 - - + +
133B VAL* 1.3 76.7 - - - +
135B GLU* 1.3 57.1 + - - +
136B GLN 2.8 12.7 + - - -
137B CYS* 3.0 24.5 + - - +
140B LYS* 4.6 21.1 - - + +
141B SER* 5.4 2.3 + - - -
160B LEU* 3.7 21.1 - - + -
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Residues in contact with GLU 135 (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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131B TYR* 2.6 54.1 + - + +
132B ALA* 3.5 25.1 - - - +
133B VAL 3.3 0.4 - - - -
134B ALA* 1.3 70.9 - - - +
136B GLN* 1.3 65.6 + - + +
137B CYS 3.6 0.9 - - - -
141B SER* 5.9 5.2 - - - -
233B PHE* 3.7 16.3 - - - -
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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