Contacts of the helix formed by residues 157 - 168 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155O GLU 3.9 1.2 + - - -
156O HIS* 1.4 71.1 - - - +
158O CYS* 1.4 56.6 - - - +
160O LEU* 3.3 15.6 + - + +
161O ASP* 3.0 62.2 + - - +
379O SER 4.0 3.6 - - - +
380O ALA* 3.4 39.9 - - + +
383O SER 4.6 1.3 - - - +
384O ALA* 3.8 20.4 - - + +
385O SER 3.4 15.8 + - - +
386O LEU* 4.1 2.8 - - - +
387O GLU 3.2 27.1 + - - -
388O PRO* 4.4 3.1 - - - -
389O SER* 3.9 28.0 - - - +
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Residues in contact with CYS 158 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4503 LYS 4.1 3.7 - - - +
4513 SER 3.3 28.5 - - - +
4523 ILE* 5.1 2.9 - - + -
128O THR* 3.9 36.6 - - + -
132O ASN* 4.2 8.1 - - - +
156O HIS* 4.3 3.6 - - + -
157O LYS* 1.4 73.9 - - - +
159O VAL* 1.4 59.4 + - + +
161O ASP* 3.4 7.4 + - - +
162O SER* 3.0 28.3 + - - -
379O SER 4.7 7.4 - - - -
383O SER* 6.0 0.4 - - - -
384O ALA* 4.2 16.1 - - - +
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Residues in contact with VAL 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128O THR 4.3 2.0 - - - +
131O ASN* 3.6 19.1 - - + +
132O ASN* 3.6 20.2 - - - +
135O ILE* 4.3 9.6 - - + -
136O LYS* 3.9 17.4 - - - +
155O GLU* 3.5 36.3 - - + +
156O HIS* 3.1 36.8 + - + +
158O CYS* 1.4 72.1 - - + +
160O LEU* 1.4 57.4 + - - +
162O SER* 3.1 4.3 + - - -
163O CYS* 3.0 27.5 + - - -
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Residues in contact with LEU 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4403 TRP* 4.5 18.4 - - + +
153O GLN 4.9 9.4 - - - +
155O GLU* 4.7 8.7 + - + +
156O HIS 3.0 12.4 + - - +
157O LYS* 3.3 25.1 + - + +
159O VAL* 1.4 73.9 - - - +
161O ASP* 1.4 62.8 + - - +
163O CYS* 3.4 20.8 - - - +
164O ARG* 3.9 8.7 + - - +
175O TYR* 3.6 39.9 + - + +
389O SER* 3.2 36.8 - - - +
391O VAL* 5.1 5.6 - - + -
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Residues in contact with ASP 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4473 ILE 4.0 8.3 - - - +
4483 ASP* 3.3 18.5 - - - +
4503 LYS* 3.3 24.5 + - - +
157O LYS* 3.0 47.9 + - - +
158O CYS* 3.4 1.2 + - - +
160O LEU* 1.4 75.4 - - - +
162O SER* 1.3 61.8 + - - +
164O ARG* 3.3 44.8 + - - +
165O SER* 5.3 0.3 - - - -
384O ALA 3.5 17.0 - - - +
386O LEU* 4.2 1.4 - - - +
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Residues in contact with SER 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4503 LYS* 3.5 31.5 - - - +
132O ASN* 3.2 16.5 + - - -
136O LYS* 3.4 25.6 - - - +
158O CYS 3.0 15.1 + - - -
159O VAL 3.1 11.3 + - - -
161O ASP* 1.3 74.8 - - - +
163O CYS* 1.3 60.4 + - - +
165O SER* 2.8 29.3 + - - -
166O LEU* 3.7 2.6 + - - +
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Residues in contact with CYS 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4443 GLN* 6.2 0.7 - - - -
136O LYS* 3.8 20.4 - - - +
151O THR* 3.8 25.1 - - - -
155O GLU* 3.8 14.6 - - - -
159O VAL* 3.0 25.1 + - - -
160O LEU* 3.4 7.9 - - - +
161O ASP 3.3 0.2 - - - -
162O SER* 1.3 74.7 - - - +
164O ARG* 1.4 57.5 + - - +
166O LEU* 3.0 24.7 + - + +
167O GLU* 3.2 9.4 + - - +
173O VAL* 4.1 13.6 - - + +
175O TYR* 3.3 23.8 - - - +
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Residues in contact with ARG 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4433 VAL* 2.9 40.2 + - - +
4443 GLN* 3.3 29.6 - - + +
4453 ASP 3.4 10.4 - - - +
4463 GLY* 3.3 7.4 + - - -
4473 ILE* 3.3 33.4 - - - +
4483 ASP* 3.5 17.3 - - - +
56A SER* 5.0 9.5 + - - -
160O LEU 3.9 7.2 - - - +
161O ASP* 3.3 37.1 + - - +
163O CYS* 1.4 73.6 - - + +
165O SER* 1.4 64.3 + - - +
167O GLU* 3.3 2.5 + - - +
168O ALA* 3.2 18.7 + - - +
175O TYR* 5.7 0.4 - - - +
386O LEU* 3.5 35.4 - - - +
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Residues in contact with SER 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4473 ILE* 3.7 23.3 + - - +
4503 LYS* 5.8 3.7 - - - +
136O LYS* 5.1 3.5 - - - +
140O ARG* 5.1 6.4 + - - -
162O SER* 2.8 22.4 + - - -
164O ARG* 1.4 78.1 - - - +
166O LEU* 1.4 58.8 + - - +
168O ALA* 3.3 5.0 + - - +
169O GLU* 3.0 30.2 + - - +
313R GLN* 3.8 25.3 - - - +
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Residues in contact with LEU 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O LYS* 3.7 43.5 - - + +
139O ALA* 4.3 6.1 - - + -
140O ARG* 3.5 43.1 - - - +
149O LEU* 4.0 30.7 - - + -
162O SER 4.5 1.8 - - - +
163O CYS* 3.0 14.2 + - + +
165O SER* 1.4 78.7 + - - +
167O GLU* 1.3 60.1 + - - +
169O GLU* 3.1 15.6 + - - +
171O PHE* 3.4 31.2 + - + +
173O VAL* 4.3 6.1 - - + -
199O LEU* 5.0 2.0 - - + -
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Residues in contact with GLU 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4443 GLN* 3.8 21.3 - - + +
4453 ASP* 3.2 42.4 - - - +
163O CYS 3.2 5.0 + - - +
164O ARG* 3.5 9.4 - - - +
166O LEU* 1.3 76.9 - - - +
168O ALA* 1.3 57.1 + - - +
170O GLY* 3.1 16.8 + - - -
171O PHE 2.9 25.7 - - - +
172O GLN* 4.2 5.2 - - - -
173O VAL* 4.0 21.2 - - + +
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Residues in contact with ALA 168 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4453 ASP 3.7 10.0 + - - +
4463 GLY* 5.0 0.7 - - - -
4473 ILE* 3.4 31.2 - - + -
164O ARG 3.2 10.2 + - - +
165O SER 3.3 11.2 + - - +
167O GLU* 1.3 72.3 - - - +
169O GLU* 1.4 55.4 + - - +
170O GLY* 3.2 8.6 + - - -
313R GLN 4.6 1.3 - - - +
314R GLU* 4.0 6.1 - - + +
317R TYR* 3.5 30.9 + - + +
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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