Contacts of the strand formed by residues 112 - 118 (chain B) in PDB entry 5IZL
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 LEU 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B ASN 3.9 1.8 + - - -
10B VAL* 3.6 23.9 - - + -
11B GLY 3.2 21.7 + - - -
110B ILE* 3.6 8.5 - - - +
111B ASP* 1.3 79.4 - - + +
113B MET* 1.3 71.4 + - - +
114B MET* 4.5 0.9 - - + +
138B CYS* 4.8 0.9 - - - -
140B LYS* 3.6 31.9 - - + +
141B LEU 4.5 0.9 - - - +
142B VAL* 4.3 13.9 - - + -
209B LEU* 3.7 27.4 - - + -
212B GLN* 4.1 32.8 - - + +
213B ILE* 4.3 13.5 - - + +
214B SER 5.6 0.7 - - - +
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Residues in contact with MET 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY 4.0 3.1 - - - -
13B LEU* 3.8 34.3 - - + -
107B ALA* 6.0 0.4 - - - -
110B ILE* 4.1 3.1 - - + -
112B LEU* 1.3 79.1 - - - +
114B MET* 1.3 63.5 + - - +
115B LEU* 4.0 20.9 - - + -
130B CYS 3.2 28.0 - - - +
131B LEU* 4.4 2.9 - - - +
134B GLY* 3.8 26.0 - - - -
138B CYS* 3.8 18.4 - - - -
140B LYS 3.2 10.0 + - - +
141B LEU* 3.3 27.0 - - + +
142B VAL 2.9 23.8 + - - -
176B PHE* 6.3 0.2 - - + -
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Residues in contact with MET 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.7 25.1 - - + -
11B GLY 3.0 14.4 + - - +
12B VAL* 3.9 11.2 - - + -
13B LEU* 3.0 28.8 + - - +
23B LEU* 4.3 12.3 - - + -
27B LEU* 4.1 8.7 - - + -
90B LEU* 3.9 20.6 - - + -
112B LEU* 4.3 1.7 - - + +
113B MET* 1.3 73.0 - - - +
115B LEU* 1.3 61.3 + - - +
116B VAL* 3.6 5.2 + - + +
142B VAL* 3.1 23.3 - - + +
144B VAL* 4.0 23.1 - - + -
205B LEU* 4.4 8.7 - - - -
209B LEU* 4.3 24.0 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU 3.7 0.7 - - - +
14B GLY* 4.1 18.6 - - - -
113B MET* 3.7 25.7 + - + -
114B MET* 1.3 70.7 - - - +
116B VAL* 1.3 65.5 + - - +
117B ILE* 3.8 17.9 + - + -
123B MET* 4.6 7.6 - - - -
127B SER* 4.0 28.5 - - - +
130B CYS* 4.1 5.4 - - + -
131B LEU* 4.2 22.0 - - + -
141B LEU* 4.0 8.5 - - + -
142B VAL 3.0 7.7 + - - +
143B VAL* 3.5 17.6 - - + +
144B VAL* 2.8 27.1 + - - +
167B MET* 4.7 4.3 - - + -
171B LEU* 6.2 0.4 - - + -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.6 27.4 - - + -
13B LEU 2.9 18.2 + - - +
14B GLY* 3.8 11.8 - - - -
15B HIS 4.3 1.9 + - - -
18B SER* 3.7 43.9 - - - +
19B GLY 4.5 8.7 - - - +
20B LYS* 4.4 2.9 - - + -
23B LEU* 4.0 17.0 - - + -
114B MET* 4.2 5.4 - - + +
115B LEU* 1.3 74.3 - - - +
117B ILE* 1.3 68.6 + - - +
127B SER* 4.5 1.4 + - - -
144B VAL* 3.5 9.9 - - + +
146B ASN* 4.1 14.1 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER* 4.6 3.8 - - - -
115B LEU* 4.2 10.8 - - + +
116B VAL* 1.3 78.2 - - - +
118B ASP* 1.3 70.2 + - - +
119B VAL* 3.4 1.2 + - - -
122B GLY* 3.5 26.5 - - - +
123B MET* 3.8 23.8 - - - -
127B SER* 3.7 24.7 - - - +
143B VAL* 4.2 19.1 - - + -
144B VAL 2.7 16.2 + - - +
145B LEU* 3.5 17.2 - - + -
146B ASN* 2.7 34.9 + - - +
163B MET* 4.8 4.3 - - + -
167B MET* 4.5 4.7 - - - -
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP 5.1 0.6 - - - +
18B SER* 4.4 12.2 - - - -
117B ILE* 1.3 73.6 - - - +
119B VAL* 1.3 54.8 + - - +
120B THR* 3.2 20.7 + - - -
121B LYS* 2.8 31.3 + - + +
122B GLY 2.7 34.2 + - - -
124B GLN* 4.2 17.7 - - - +
146B ASN 3.9 2.7 - - - -
147B LYS* 3.4 45.9 + - - +
150B LEU* 5.3 0.5 - - - +
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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