Contacts of the helix formed by residues 157 - 168 (chain M) in PDB entry 5KZ5
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 LYS 157 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4511 SER 5.2 0.4 - - - -
156M HIS* 1.3 70.7 + - - +
158M CYS* 1.3 56.3 + - - +
159M VAL 3.3 0.2 - - - -
160M LEU* 3.7 6.5 - - - -
161M ASP* 2.8 34.7 + - + +
378M GLY* 4.3 8.7 + - - +
379M SER 4.1 4.9 - - - +
380M ALA* 3.9 21.8 - - - +
384M ALA* 3.8 24.5 - - + -
387M GLU* 3.5 26.6 - - - +
388M PRO 3.0 23.8 + - - -
389M SER* 3.8 13.4 - - - +
390M TYR* 3.3 36.1 - - + +
391M VAL* 3.5 17.7 - - + +
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Residues in contact with CYS 158 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4501 LYS* 5.1 0.2 - - - -
4511 SER 3.9 16.2 + - - +
4521 ILE* 3.8 42.8 - - + -
4541 TRP* 5.2 3.0 - - + -
128M THR* 4.0 25.1 - - + -
132M ASN* 4.5 3.7 + - - +
156M HIS* 4.5 12.1 - - + +
157M LYS* 1.3 76.1 - - - +
159M VAL* 1.4 64.6 + - + +
161M ASP* 3.5 1.7 + - - +
162M SER* 3.1 24.1 + - - -
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Residues in contact with VAL 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M THR* 4.9 6.1 - - + +
131M ASN* 3.6 34.1 - - + +
132M ASN* 4.4 7.9 - - - +
135M ILE* 3.7 30.7 - - + -
136M LYS* 5.8 0.4 - - - -
155M GLU* 3.7 24.0 - - + +
156M HIS* 3.0 17.9 + - + +
158M CYS* 1.4 78.9 - - + +
160M LEU* 1.4 57.3 + - - +
162M SER* 2.7 23.0 + - - +
163M CYS* 3.0 25.9 + - - -
207M ASN* 5.3 0.9 - - - +
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Residues in contact with LEU 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M THR* 4.7 3.6 - - + -
152M THR 3.5 15.3 - - - +
153M GLN* 4.0 13.5 - - - +
155M GLU* 3.4 44.4 - - + +
156M HIS 3.7 8.5 - - - +
157M LYS* 3.4 7.1 + - - +
159M VAL* 1.4 76.7 - - - +
161M ASP* 1.3 55.3 + - - +
163M CYS* 3.4 6.6 + - - +
164M ARG* 3.2 22.5 + - - +
175M TYR* 3.5 36.4 + - + +
390M TYR* 3.7 33.6 - - + -
391M VAL* 3.8 12.3 - - + -
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Residues in contact with ASP 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4481 ASP* 3.5 17.2 - - - +
4491 LEU* 3.2 33.3 - - - +
4511 SER* 3.6 14.7 - - - +
157M LYS* 2.8 25.6 + - + +
158M CYS 4.1 2.9 - - - +
160M LEU* 1.3 71.6 - - - +
162M SER* 1.4 63.7 + - - +
164M ARG* 3.5 15.2 + - - +
165M SER 3.9 2.6 + - - -
384M ALA* 2.9 27.9 - - + +
385M SER* 4.4 1.2 - - - -
387M GLU* 3.5 18.9 - - + +
390M TYR* 5.0 3.5 - - + -
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Residues in contact with SER 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4501 LYS* 3.5 26.8 - - - +
132M ASN* 3.3 31.3 + - - -
136M LYS* 3.4 14.0 - - - -
158M CYS 3.1 15.7 + - - -
159M VAL* 2.7 21.1 + - - +
161M ASP* 1.4 74.9 - - - +
163M CYS* 1.4 57.0 + - - +
165M SER* 2.9 22.5 + - - -
166M LEU* 3.6 9.9 - - - +
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Residues in contact with CYS 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135M ILE* 4.4 7.0 - - - -
136M LYS* 3.4 24.9 - - - +
151M THR* 3.9 24.9 - - + -
155M GLU* 4.6 0.7 - - - -
159M VAL* 3.0 34.2 + - - -
160M LEU* 3.5 12.1 - - - +
162M SER* 1.4 72.6 + - - +
164M ARG* 1.4 64.1 + - - +
165M SER 3.3 0.2 - - - -
166M LEU* 3.2 7.8 + - - +
167M GLU 3.2 16.5 + - - -
173M VAL* 3.8 26.3 - - + +
175M TYR* 5.3 2.0 - - + -
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Residues in contact with ARG 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4431 VAL 3.8 5.4 - - - -
4441 GLN* 3.2 34.9 + - - +
4461 GLY* 4.0 11.2 - - - -
4471 ILE* 3.2 25.5 - - - +
160M LEU 3.2 11.9 + - - +
161M ASP* 3.6 17.7 - - - +
162M SER 3.3 0.6 - - - -
163M CYS* 1.4 75.3 - - - +
165M SER* 1.4 60.7 + - - +
167M GLU* 3.0 46.8 + - - +
168M ALA* 3.2 11.4 + - - +
173M VAL* 3.8 13.9 + - - +
175M TYR* 3.1 52.3 + - - -
387M GLU* 4.4 6.5 - - - +
390M TYR* 3.6 19.4 + - - -
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Residues in contact with SER 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4471 ILE 3.8 2.3 + - - -
4481 ASP 3.4 21.3 - - - -
4491 LEU* 4.2 11.5 - - - -
4501 LYS* 4.5 5.9 - - - -
161M ASP 3.9 2.0 + - - -
162M SER* 2.9 22.3 + - - -
164M ARG* 1.4 77.1 - - - +
166M LEU* 1.4 62.1 + - - +
168M ALA* 3.4 3.1 + - - +
169M GLU* 3.2 17.3 + - - +
312T GLN* 3.6 16.9 + - - -
313T GLN* 3.3 32.8 - - - +
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Residues in contact with LEU 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4501 LYS* 6.1 0.9 - - - -
136M LYS* 3.7 29.6 - - + +
139M ALA* 6.2 0.9 - - + -
140M ARG* 3.6 42.0 - - - +
149M LEU* 4.9 10.5 - - + -
162M SER 3.6 17.0 - - - +
163M CYS* 3.2 10.8 + - - +
165M SER* 1.4 74.9 - - - +
167M GLU* 1.4 64.5 + - - +
169M GLU* 3.1 25.5 + - - +
171M PHE* 3.3 31.9 + - + +
173M VAL* 5.0 0.9 - - + -
312T GLN* 3.5 22.0 - - - +
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Residues in contact with GLU 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4441 GLN 3.0 16.7 - - - +
4451 ASP* 2.9 27.4 - - - +
163M CYS 3.2 6.4 + - - +
164M ARG* 3.0 33.6 + - - +
166M LEU* 1.4 76.2 - - - +
168M ALA* 1.4 56.6 + - - +
170M GLY* 3.1 11.8 + - - -
171M PHE 3.1 29.9 - - - +
172M GLN* 4.6 1.1 - - - -
173M VAL* 3.2 34.5 + - + +
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Residues in contact with ALA 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4451 ASP 5.1 4.2 + - - -
4461 GLY* 5.2 1.1 - - - -
4471 ILE* 3.9 22.7 - - + -
164M ARG 3.2 11.3 + - - +
165M SER* 3.5 12.6 - - - +
167M GLU* 1.4 73.5 - - - +
169M GLU* 1.4 56.3 + - - +
170M GLY* 3.1 6.4 + - - -
313T GLN* 3.5 7.3 - - + +
314T GLU* 3.7 28.5 - - - +
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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