Contacts of the strand formed by residues 140 - 147 (chain C) in PDB entry 1ZQ1
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 ILE 140 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.1 19.7 - - + -
53A ASN* 4.1 4.9 - - - +
55A TYR* 3.6 37.9 - - + +
56A ASN 5.3 3.7 + - - +
57A ILE* 3.6 28.7 - - + +
116C VAL* 4.0 11.3 - - + +
119C VAL* 3.7 14.2 - - - +
120C TYR 4.6 2.7 + - - +
139C ALA* 1.3 74.7 - - - +
141C ILE* 1.3 65.9 + - - +
142C ALA 3.9 15.9 - - - +
143C THR* 3.9 6.1 - - + -
158C THR* 3.4 23.1 - - + +
159C ILE 3.7 3.1 - - - +
160C CYS* 3.5 18.4 - - - -
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Residues in contact with ILE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 3.7 17.0 - - + -
104C ALA* 4.0 17.5 - - + -
105C LEU* 4.1 26.2 - - + +
115C PRO* 3.3 3.3 - - - +
116C VAL* 2.7 36.1 + - - +
119C VAL* 4.2 19.7 - - + -
121C TYR* 4.6 4.0 - - + +
139C ALA 4.2 6.5 - - - +
140C ILE* 1.3 80.2 - - - +
142C ALA* 1.3 59.6 + - + +
159C ILE* 2.8 15.0 + - + +
161C LEU* 3.4 43.1 - - + +
443C ILE* 5.0 1.0 - - - +
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA* 3.4 33.2 - - + -
113C ALA* 3.5 12.8 - - + -
114C LYS 3.7 6.3 - - - -
115C PRO* 3.9 7.6 - - + -
116C VAL* 4.3 1.3 - - - +
140C ILE* 3.9 1.9 - - - +
141C ILE* 1.3 79.4 - - + +
143C THR* 1.3 72.2 + - - +
158C THR* 3.8 0.2 - - - -
159C ILE* 3.1 34.7 + - + +
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Residues in contact with THR 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.5 2.8 - - - +
31A TYR* 3.5 24.6 + - + -
51A LEU* 5.1 4.5 - - + -
57A ILE* 4.4 10.8 - - + -
113C ALA* 3.7 1.5 - - - -
114C LYS* 2.9 35.3 + - - +
116C VAL* 5.0 2.1 - - + +
140C ILE* 3.9 21.1 - - + -
142C ALA* 1.3 85.4 - - - +
144C ASP* 1.3 82.2 + - - +
145C GLY 3.3 2.6 + - - -
156C ILE 4.1 1.3 - - - -
157C PRO 3.5 15.7 - - - +
158C THR* 4.6 4.0 - - - +
159C ILE* 5.7 0.2 - - - -
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Residues in contact with ASP 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.4 10.5 - - + +
30A THR* 3.8 25.0 + - - +
31A TYR* 4.8 1.6 - - - -
114C LYS* 3.0 32.7 + - + +
143C THR* 1.3 85.0 + - - +
145C GLY* 1.3 64.4 + - - +
156C ILE 3.3 11.2 + - - -
157C PRO* 3.4 12.2 + - - +
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Residues in contact with GLY 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU 3.6 2.5 - - - -
112C ASN 3.2 22.7 - - - -
113C ALA* 3.6 8.0 - - - +
143C THR 3.3 2.2 + - - -
144C ASP* 1.3 78.8 - - - +
146C LYS* 1.3 66.4 + - - +
155C GLY* 3.8 2.4 - - - -
156C ILE* 2.9 34.7 + - - -
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU 3.1 10.6 + - - +
112C ASN* 2.9 43.3 + - + +
145C GLY* 1.3 75.7 - - - +
147C VAL* 1.3 64.8 + - - +
148C GLU* 2.7 42.8 + - - +
153C ALA* 4.2 11.1 - - + +
154C VAL 3.3 13.7 - - - +
155C GLY* 4.2 4.5 - - - -
156C ILE* 4.3 3.6 - - - +
208C PHE* 4.9 0.5 - - - -
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 3.9 10.3 - - + -
112C ASN* 5.2 0.2 - - - +
146C LYS* 1.3 76.3 - - - +
148C GLU* 1.3 74.7 + - - +
149C THR* 3.8 1.4 + - - -
153C ALA* 4.5 1.1 - - - -
154C VAL* 2.8 36.4 + - - +
156C ILE* 3.8 17.9 - - + +
204C VAL* 4.8 2.0 - - + +
205C VAL* 4.1 26.0 - - + +
208C PHE* 3.3 51.1 - - + -
209C ILE* 4.2 8.5 - - + -
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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