Contacts of the strand formed by residues 146 - 153 (chain A) in PDB entry 4ZIN
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A CH6 3.1 28.4 + - - -
144A GLU 3.8 2.6 + - - -
145A ALA* 1.3 76.6 - - - +
147A SER* 1.3 63.0 + - - +
161A ILE* 3.7 9.5 - - - +
162A LYS 4.3 5.3 + - - -
163A GLN* 2.3 30.6 + - - -
164A ARG 5.0 0.7 + - - -
196A ASN* 3.6 3.6 - - - +
197A ILE* 2.9 31.2 + - - +
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER* 1.3 77.1 - - - +
148A GLU* 1.3 61.9 + - - +
149A ARG* 3.8 8.1 + - - +
160A GLU 3.9 3.1 - - - +
161A ILE* 3.5 18.5 - - - +
162A LYS 4.8 1.6 + - - -
194A ASN* 3.9 20.6 + - - +
195A VAL 3.2 5.1 + - - -
196A ASN* 3.6 18.1 + - - -
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A CH6 5.3 0.2 - - - +
70A LYS* 2.7 33.4 + - - -
95A ARG* 4.8 0.6 + - - -
147A SER* 1.3 73.0 - - - +
149A ARG* 1.3 63.7 + - - +
150A MET* 3.4 26.5 + - - +
159A GLY* 3.5 16.6 - - - +
160A GLU 3.5 9.4 - - - +
161A ILE* 3.5 29.2 - - + +
179A THR* 4.4 3.5 + - - -
181A TYR* 2.8 20.5 + - - -
194A ASN* 3.4 3.3 - - - -
195A VAL* 2.8 44.3 + - + +
197A ILE* 4.0 9.3 - - + +
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A SER* 4.8 8.1 - - - +
148A GLU* 1.3 71.9 - - - +
150A MET* 1.3 60.8 + - - +
151A TYR* 4.3 7.5 - - + -
158A LYS 3.8 0.3 - - - +
159A GLY* 3.3 2.1 - - - -
160A GLU* 2.9 49.2 + - + +
193A TYR 4.8 0.2 - - - +
194A ASN* 3.5 22.2 + - - +
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Residues in contact with MET 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 6.0 1.6 - - + -
83A LEU* 6.3 0.2 - - + -
148A GLU* 3.4 43.5 - - - +
149A ARG* 1.3 74.6 - - - +
151A TYR* 1.3 62.7 + - - +
157A LEU* 3.8 26.9 - - + -
158A LYS 3.1 19.3 - - - +
159A GLY* 3.9 7.2 - - - -
181A TYR* 3.9 15.9 - - + -
191A GLY 4.7 0.2 - - - -
192A ALA* 3.2 6.6 - - - +
193A TYR* 2.8 71.0 + - + +
195A VAL* 3.9 11.7 - - + -
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Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG* 4.3 7.2 - - + -
150A MET* 1.3 79.6 - - - +
152A PRO* 1.3 83.0 - - + +
153A GLU* 3.6 24.8 + - + -
157A LEU* 3.9 6.3 - - - +
158A LYS* 2.8 49.3 + - + -
160A GLU* 2.7 40.2 + - + -
178A LYS* 3.4 20.1 + - - -
191A GLY 4.3 1.8 - - - -
192A ALA* 4.5 9.2 - - + -
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Residues in contact with PRO 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 1.3 95.2 - - + +
153A GLU* 1.3 63.4 + - - +
156A ALA 3.4 9.4 - - - +
157A LEU* 4.5 3.1 - - + -
189A LEU* 4.2 20.4 - - + -
190A PRO 3.2 27.1 - - - +
191A GLY* 3.7 16.4 - - - +
192A ALA* 4.2 1.1 - - + +
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 3.6 23.9 + - + -
152A PRO* 1.3 75.8 - - - +
154A ASP* 1.3 82.4 + - + +
155A GLY 3.2 1.5 - - - +
156A ALA* 2.8 23.7 + - - +
158A LYS* 3.1 40.5 + - + +
178A LYS* 4.7 5.2 + - - -
189A LEU* 5.2 0.2 - - - +
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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