Contacts of the strand formed by residues 156 - 163 (chain U) in PDB entry 4ZKO
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 156 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16U ILE* 3.0 31.8 + - + +
18U GLY* 2.8 33.9 + - - +
19U GLY 4.6 1.1 + - - -
20U GLU* 3.3 17.5 - - - +
21U PHE* 3.5 32.5 - - + +
22U THR* 3.9 3.8 - - - -
139U THR* 3.4 8.0 - - - +
140U GLY 3.0 38.1 + - - +
144U GLU* 2.8 40.2 + - + +
152U PRO* 4.4 6.5 - - + -
154U GLN 3.7 3.4 - - - +
155U LEU* 1.3 73.0 - - - +
157U MET* 1.3 61.9 + - - +
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Residues in contact with MET 157 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16U ILE* 4.2 4.5 - - - -
19U GLY* 3.5 0.9 - - - -
20U GLU* 2.9 54.0 + - + +
22U THR* 3.8 27.8 - - + -
26U ASN* 4.5 13.5 - - - +
27U GLN* 4.0 12.6 - - - +
137U GLU* 3.5 45.5 - - + +
138U ILE 3.1 11.4 - - - +
139U THR* 3.8 6.7 - - - +
156U LYS* 1.3 76.2 - - - +
158U THR* 1.3 62.3 + - - +
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Residues in contact with THR 158 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16U ILE* 3.6 11.7 - - + -
19U GLY* 3.3 16.0 - - - -
20U GLU* 5.4 2.7 - - - -
137U GLU* 3.2 7.6 - - - +
138U ILE* 3.0 59.0 + - + +
157U MET* 1.3 79.1 - - - +
159U VAL* 1.3 74.3 + - - +
160U VAL* 4.5 1.3 - - + -
188U THR* 2.6 36.0 + - - +
189U ASP 4.3 5.2 - - - +
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Residues in contact with VAL 159 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U GLU* 6.2 0.2 - - - +
135U SER* 3.8 26.9 - - - +
136U CYS 3.2 13.7 - - - +
137U GLU* 4.8 8.1 - - + +
158U THR* 1.3 80.6 + - - +
160U VAL* 1.3 73.4 + - - +
161U LYS* 5.5 2.2 - - + -
185U ASP* 4.6 4.3 - - - +
188U THR* 3.6 16.5 - - - +
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Residues in contact with VAL 160 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134U THR 3.9 0.2 - - - +
135U SER* 3.6 0.9 - - - -
136U CYS* 2.8 36.1 + - - +
138U ILE* 4.2 30.1 - - + -
158U THR* 4.5 3.6 - - + -
159U VAL* 1.3 80.8 - - - +
161U LYS* 1.3 63.0 + - - +
162U LEU 4.2 0.2 + - - -
183U ALA* 3.7 21.5 - - + +
184U ALA* 3.9 23.1 - - - +
185U ASP* 4.3 1.1 - - - +
188U THR* 4.1 19.1 - - + +
189U ASP* 4.5 4.3 - - - +
199U LEU* 4.1 18.8 - - + -
228U TYR* 4.4 3.4 - - - +
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Residues in contact with LYS 161 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133U GLY* 3.7 24.3 + - - +
134U THR 3.3 5.6 - - - +
135U SER* 3.6 26.2 - - - +
159U VAL* 5.5 1.8 - - + -
160U VAL* 1.3 74.3 - - - +
162U LEU* 1.3 65.4 + - - +
163U ILE* 3.5 3.4 + - + +
183U ALA* 3.2 3.9 - - - -
184U ALA 2.9 37.2 + - - +
185U PRO* 4.0 29.5 - - - +
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Residues in contact with LEU 162 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129U ASP* 5.7 0.2 - - + -
130U PRO* 3.7 50.3 - - + +
131U GLN 4.2 2.2 - - - +
132U PHE* 3.7 23.0 - - + +
133U GLY* 2.8 25.9 + - - +
134U THR* 3.0 13.5 + - - +
136U CYS* 3.8 24.7 - - + -
161U LYS* 1.3 73.3 - - - +
163U ILE* 1.3 61.4 + - - +
181U LEU* 5.3 9.4 - - + -
182U CYS 3.6 6.1 - - - +
183U ALA* 4.0 17.0 - - + -
199U LEU* 4.1 17.7 - - + -
201U CYS* 4.2 1.3 - - - -
210U THR* 4.9 3.8 - - + -
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Residues in contact with ILE 163 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132U PHE* 3.1 16.3 - - - -
161U LYS* 3.7 6.7 - - + +
162U LEU* 1.3 76.2 - - - +
164U SER* 1.3 76.8 + - - +
165U HIS* 4.7 0.2 - - - -
167U GLU* 3.6 32.8 - - + +
168U CYS* 4.0 12.8 - - + +
171U TYR* 4.5 8.7 - - + +
182U CYS* 2.9 25.5 + - + +
183U ALA 4.1 0.2 - - - -
184U ALA* 3.6 27.6 - - + +
186U TRP* 4.7 2.9 - - + -
225U PRO* 3.6 28.3 - - + -
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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