Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 1ZK2
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 ALA 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER 3.0 16.4 - - - +
128A MET* 3.8 33.7 - - + +
133A LEU* 3.3 6.5 - - + -
134A GLY* 1.3 78.7 - - - +
136A SER* 1.3 60.0 + - - +
179A ASP 3.1 19.7 + - - +
180A VAL* 3.5 10.5 - - + -
181A ARG* 3.0 28.0 + - - +
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Residues in contact with SER 136 (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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84A SER 3.1 6.6 + - - -
85A THR* 3.3 9.9 - - - +
86A LEU 3.0 24.3 + - - +
128A MET* 4.4 0.6 - - - +
134A GLY 4.4 0.7 - - - -
135A ALA* 1.3 76.6 - - - +
137A ILE* 1.3 64.3 + - - +
138A ILE* 3.9 9.6 + - - +
181A ARG* 3.5 22.0 + - - +
183A ASN* 5.2 1.9 + - - -
229A LEU* 2.7 30.6 + - - +
230A ALA* 4.1 14.1 - - - -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.3 14.4 - - + +
88A ASN* 4.1 5.6 - - - +
121A THR* 3.8 34.3 - - + +
124A GLY* 4.1 3.1 - - - -
125A ILE* 3.9 25.6 - - + +
128A MET* 3.6 21.8 - - + -
136A SER* 1.3 73.9 + - - +
138A ILE* 1.3 64.8 + - - +
139A ASN* 3.5 28.3 - - - +
180A VAL* 3.9 13.0 - - + -
181A ARG 2.8 12.5 + - - +
182A VAL* 3.3 10.1 - - + +
183A ASN* 3.1 25.8 + - - +
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Residues in contact with ILE 138 (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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85A THR* 4.8 2.7 - - + -
86A LEU 2.8 11.1 + - - +
87A VAL* 3.3 22.4 - - + +
88A ASN 2.9 24.9 + - - -
136A SER* 3.9 10.5 - - - +
137A ILE* 1.3 75.6 - - - +
139A ASN* 1.3 62.9 + - - +
140A MET* 4.4 7.0 - - + -
183A ASN* 3.6 5.8 - - + +
185A VAL* 3.7 30.1 - - + -
226A CYS* 3.5 40.2 - - + +
229A LEU* 3.7 22.2 - - + -
230A ALA* 3.7 16.4 - - + +
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Residues in contact with ASN 139 (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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88A ASN* 2.8 30.6 + - - +
117A VAL* 3.7 13.5 - - + +
121A THR* 3.1 20.4 + - - +
137A ILE* 3.5 8.9 - - - +
138A ILE* 1.3 71.4 - - - +
140A MET* 1.3 62.6 + - - +
141A SER 3.2 3.1 + - - -
162A VAL* 3.7 12.3 - - + -
165A MET* 4.7 1.6 - - - +
166A SER* 2.9 29.1 + - - +
182A VAL* 4.0 13.5 - - - +
183A ASN 2.9 10.9 + - - +
184A THR* 3.1 7.3 - - + -
185A VAL 3.1 22.5 + - - -
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Residues in contact with MET 140 (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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18A ILE* 4.7 2.9 - - + -
22A ILE* 4.3 4.0 - - + -
87A VAL* 4.2 16.6 - - + -
88A ASN 3.0 21.5 + - - +
89A ASN* 3.7 30.3 - - - +
117A VAL* 5.6 3.5 - - - +
138A ILE* 3.9 3.9 + - + -
139A ASN* 1.3 70.0 - - - +
141A SER* 1.3 69.6 + - - +
159A LYS* 3.6 17.8 + - - +
162A VAL* 4.6 8.6 - - - +
185A VAL* 3.9 23.1 - - + +
187A PRO* 3.9 30.3 - - + -
222A ILE* 4.0 5.4 - - - -
226A CYS* 4.0 21.5 - - - -
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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