Contacts of the helix formed by residues 137 - 151 (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 CYS 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL 4.1 5.1 + - - +
134B ALA* 3.0 12.7 + - - +
135B GLU 5.3 0.4 - - - -
136B GLN* 1.3 77.2 - - - +
138B PRO* 1.3 60.1 - - - +
139B VAL* 3.2 36.6 - - - -
140B LYS* 2.9 39.4 + - + +
141B SER* 3.5 4.1 + - - -
233B PHE* 5.2 0.7 - - - -
290B ARG* 3.5 17.0 - - - +
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Residues in contact with PRO 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLN 3.6 9.2 - - - +
137B CYS* 1.3 78.8 - - - +
139B VAL* 1.3 64.9 + - - +
140B LYS 3.1 0.4 - - - -
141B SER* 3.6 11.9 - - - -
142B ALA* 3.0 25.5 + - - +
233B PHE* 3.7 18.8 - - + -
236B ASP* 3.9 25.6 - - + +
238B VAL* 3.7 21.2 - - + +
290B ARG* 3.9 26.5 - - - +
356B VAL* 4.0 14.2 - - + +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B CYS* 3.2 24.5 - - - -
138B PRO* 1.3 78.6 - - - +
140B LYS* 1.3 67.7 + - + +
142B ALA* 3.5 4.0 + - - -
143B GLU* 3.0 27.4 + - - +
238B VAL* 4.4 7.2 - - + -
272B SER* 5.8 2.5 - - - -
273B SER* 6.2 2.0 - - - -
288B PHE* 3.6 26.6 - - + -
290B ARG* 3.5 41.3 - - + +
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Residues in contact with LYS 140 (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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134B ALA* 4.6 24.0 - - + +
137B CYS* 2.9 21.9 + - + +
139B VAL* 1.3 88.1 - - + +
141B SER* 1.3 57.7 + - - +
142B ALA 3.3 0.2 - - - -
143B GLU* 3.8 14.9 - - + +
144B ASP* 3.2 30.0 + - - +
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA 5.4 2.2 + - - -
135B GLU* 5.9 4.7 - - - -
137B CYS 3.5 4.2 + - - -
138B PRO* 3.3 16.5 + - - -
140B LYS* 1.3 76.4 - - - +
142B ALA* 1.3 64.6 + - - +
143B GLU 3.3 0.2 - - - -
144B ASP* 3.8 6.0 - - - +
145B GLN* 3.2 28.8 + - - +
231B VAL* 4.5 17.2 - - - +
233B PHE* 5.7 6.0 - - - -
356B VAL* 4.5 8.7 - - - +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO 3.0 18.1 + - - +
139B VAL* 3.6 6.5 - - - +
141B SER* 1.3 78.0 - - - +
143B GLU* 1.3 56.9 + - - +
145B GLN* 3.4 3.8 + - - +
146B LEU* 2.9 27.5 + - - +
238B VAL* 4.4 8.3 - - + +
240B ALA* 4.5 2.7 - - + -
288B PHE* 4.1 16.2 - - + -
354B VAL* 3.6 19.6 - - + +
356B VAL* 3.9 19.3 - - + +
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Residues in contact with GLU 143 (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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84B ARG* 3.9 13.9 + - - +
139B VAL 3.0 17.3 + - - +
140B LYS* 4.1 14.9 - - - +
141B SER 3.3 0.2 - - - -
142B ALA* 1.3 76.1 - - - +
144B ASP* 1.3 64.3 + - - +
146B LEU* 3.5 4.5 + - - +
147B TYR* 3.3 42.4 + - + -
159B LEU* 5.9 1.4 - - - +
275B LYS* 2.9 34.2 + - - +
277B ASP* 4.8 1.1 - - - -
286B THR* 4.9 2.2 - - + -
288B PHE* 3.6 20.7 - - + -
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Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 3.2 29.5 + - - +
140B LYS 3.2 18.8 + - - +
141B SER* 3.9 7.9 - - - +
142B ALA 3.3 0.4 - - - -
143B GLU* 1.3 78.7 - - - +
145B GLN* 1.3 65.9 + - + +
147B TYR* 3.8 2.4 + - - +
148B ALA* 3.2 22.3 + - - +
156B GLY 5.0 0.9 - - - +
158B PRO* 4.6 6.7 - - - +
159B LEU* 4.1 23.6 + - - +
160B LEU* 5.1 2.8 + - - +
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Residues in contact with GLN 145 (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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141B SER* 3.2 20.4 + - - +
142B ALA* 3.6 6.5 - - - +
144B ASP* 1.3 80.2 + - - +
146B LEU* 1.3 64.1 + - - +
148B ALA* 3.2 9.9 + - - +
149B ILE* 2.9 30.8 + - - +
229B ASN* 2.6 37.4 + - + +
231B VAL* 4.0 25.2 - - + +
354B VAL* 3.8 17.0 - - + -
356B VAL* 5.5 0.4 - - + -
230M ARG 4.8 2.9 + - - +
232M ARG* 5.1 15.6 - - - +
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Residues in contact with LEU 146 (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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142B ALA 2.9 9.6 + - - +
143B GLU* 3.5 7.4 - - - +
145B GLN* 1.3 76.8 - - - +
147B TYR* 1.3 61.5 + - + +
149B ILE* 3.4 4.6 - - + +
150B THR* 3.0 33.3 + - + +
240B ALA* 4.1 7.9 - - + +
241B ILE 4.0 12.1 - - - +
242B GLY* 3.8 24.0 - - - +
284B LEU* 4.4 7.2 - - + -
286B THR* 3.5 28.0 - - + -
288B PHE* 3.9 24.0 - - + -
352B ASN* 4.2 7.4 - - + +
354B VAL* 3.4 34.3 - - + -
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Residues in contact with TYR 147 (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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84B ARG* 3.7 45.1 - - + +
143B GLU* 3.3 34.6 + - + +
144B ASP 4.1 1.1 - - - +
146B LEU* 1.3 80.1 - - + +
148B ALA* 1.3 62.2 + - - +
150B THR* 3.8 6.3 - - - -
151B PHE* 3.1 28.7 + + - -
155B LEU* 3.4 31.9 - - + +
156B GLY* 3.0 15.0 + - - -
277B ASP* 2.6 43.9 + - - +
279B PHE* 3.6 18.9 - + - -
284B LEU* 3.5 22.8 - - + +
286B THR* 4.8 1.1 - - + -
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Residues in contact with ALA 148 (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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144B ASP 3.2 17.0 + - - +
145B GLN* 3.2 17.2 + - - +
147B TYR* 1.3 79.5 - - - +
149B ILE* 1.3 62.2 + - + +
152B ARG* 3.6 23.2 - - - +
156B GLY* 3.5 21.7 - - - +
364M TYR* 4.5 7.4 + - - -
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Residues in contact with ILE 149 (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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145B GLN 2.9 19.1 + - - +
146B LEU* 3.4 9.6 - - - +
148B ALA* 1.3 78.7 - - + +
150B THR* 1.3 66.9 + - - +
152B ARG* 4.0 10.2 + - - +
224B PHE* 3.9 11.3 - - - +
227B GLU* 3.7 47.2 - - + +
228B GLU* 4.3 3.4 - - - -
229B ASN* 4.2 27.4 - - + +
352B ASN* 4.0 13.5 - - + -
353B TYR 4.1 2.5 - - - +
354B VAL* 3.6 29.2 - - + -
230M ARG* 5.9 6.1 - - - -
364M TYR* 6.3 0.9 - - - -
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Residues in contact with THR 150 (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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146B LEU* 3.0 21.2 + - - +
147B TYR* 3.5 1.4 + - - -
149B ILE* 1.3 81.8 - - - +
151B PHE* 1.3 92.0 + - - +
152B ARG 3.3 1.0 + - - -
223B PHE 2.6 27.2 - - - +
224B PHE* 3.2 14.8 - - - -
242B GLY* 4.3 4.3 - - - +
244B PRO* 4.8 3.1 - - + -
284B LEU* 3.8 20.2 - - + +
352B ASN* 3.0 37.0 - - + +
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Residues in contact with PHE 151 (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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147B TYR* 3.1 32.0 + + - -
150B THR* 1.3 92.2 + - - +
152B ARG* 1.3 66.8 + - - +
153B LYS 3.2 2.1 + - - -
154B GLY* 3.4 5.0 + - - +
155B LEU* 3.5 45.3 - - + +
156B GLY 2.8 15.9 + - - -
221B PRO* 4.6 13.0 - - + +
222B LYS* 3.7 22.2 - - - -
223B PHE* 4.5 6.7 - + - -
224B PHE* 5.1 1.1 - - - -
244B PRO* 3.8 21.5 - - + -
279B PHE* 5.1 0.7 - + - -
283B GLY* 4.1 13.7 - - - -
284B LEU* 3.5 31.9 - - + -
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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