Contacts of the helix formed by residues 142 - 149 (chain C) in PDB entry 1SZU
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 THR 142 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C SER* 4.0 19.7 - - - -
113C GLU* 5.5 1.1 - - + +
116C GLU* 2.6 29.2 + - + +
141C ARG* 1.3 82.2 - - - +
143C HIS* 1.3 69.0 + - - +
145C THR* 2.4 30.5 + - - +
146C LEU* 2.8 21.5 + - - +
113D GLU* 5.0 11.9 - - + +
116D GLU* 3.6 26.5 - - + -
142D THR* 4.2 11.9 - - + -
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Residues in contact with HIS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ARG 4.2 0.2 + - - -
142C THR* 1.3 73.4 - - - +
144C TYR* 1.3 63.3 + - - +
146C LEU* 3.1 5.5 + - - +
147C ALA 3.1 15.2 + - - -
162C MET* 3.8 23.7 - - + +
163C PRO* 3.7 23.6 - - + +
116D GLU* 2.7 38.5 + - - +
119D VAL* 3.6 25.4 - - + +
120D LYS* 3.7 23.2 - - + +
123D ARG* 3.1 40.7 + - - -
144D TYR* 3.8 32.9 - + + -
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Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLU* 3.5 18.2 + - - +
119C VAL* 3.9 22.1 - - + +
123C ARG* 4.7 4.4 + - - -
129C SER 4.5 5.5 + - - -
131C THR* 2.6 35.2 + - - +
142C THR* 3.3 1.8 + - - -
143C HIS* 1.3 79.9 - - - +
145C THR* 1.3 63.4 + - + +
147C ALA* 3.1 4.8 + - - +
148C LEU* 3.1 46.7 + - + +
163C PRO* 4.2 19.9 - - + +
164C GLY 4.6 7.0 - - - -
165C HIS* 4.3 4.0 + - + -
166C VAL* 3.7 18.2 - - + +
116D GLU* 5.0 0.8 + - - -
143D HIS* 3.8 43.7 - + + -
144D TYR* 5.2 0.8 - - - +
163D PRO* 4.8 3.1 - - + -
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Residues in contact with THR 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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112C SER* 3.8 19.0 - - - +
115C VAL* 3.9 20.0 - - + -
116C GLU* 4.1 7.6 - - + +
139C HIS* 3.2 29.4 - - + +
140C GLY* 3.2 8.1 - - - -
141C ARG 3.4 0.3 + - - -
142C THR* 2.4 47.4 + - - +
144C TYR* 1.3 74.0 - - + +
146C LEU* 1.3 55.0 + - - +
148C LEU* 3.7 8.4 - - + +
149C THR* 2.6 37.2 + - - -
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Residues in contact with LEU 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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140C GLY 3.6 13.0 - - - +
141C ARG* 3.7 24.5 - - + +
142C THR 2.8 21.6 + - - +
143C HIS 3.4 4.5 - - - +
145C THR* 1.3 73.6 - - - +
147C ALA* 1.3 65.9 + - - +
149C THR* 3.1 22.6 + - - +
151C LYS 4.8 2.3 - - - +
155C TYR* 3.5 48.5 - - + +
156C SER* 3.7 18.2 + - - +
159C MET* 4.8 0.4 - - - -
162C MET* 3.9 21.1 - - + +
120D LYS* 3.9 19.1 - - + -
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Residues in contact with ALA 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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193A ASN 5.1 0.2 - - - +
194A ASP* 4.0 4.2 - - - +
143C HIS 3.1 10.3 + - - +
144C TYR* 3.1 13.3 + - - +
146C LEU* 1.3 78.3 - - - +
148C LEU* 1.3 51.9 + - - +
149C THR 3.4 0.5 - - - +
162C MET* 4.1 12.9 - - + +
163C PRO* 3.3 27.8 - - + +
166C VAL* 3.6 21.0 - - + +
168C ARG* 2.7 31.2 + - - -
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Residues in contact with LEU 148 (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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115C VAL* 3.7 30.1 - - + -
119C VAL* 4.2 6.3 - - + -
131C THR* 3.5 29.4 - - - +
132C ILE 5.0 0.2 - - - +
133C ALA* 3.2 18.7 - - + +
137C ALA* 4.2 0.5 - - - +
139C HIS* 3.7 19.8 - - + -
144C TYR* 3.1 38.7 + - + +
145C THR* 3.7 9.2 - - - +
146C LEU 3.3 0.2 - - - -
147C ALA* 1.3 75.5 - - - +
149C THR* 1.3 57.6 + - - +
150C GLY 3.3 0.3 + - - -
166C VAL* 3.6 14.6 - - + -
168C ARG* 2.7 28.1 + - - -
204C VAL* 4.4 11.7 - - + -
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Residues in contact with THR 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN 3.6 4.7 - - - +
137C ALA 3.2 20.0 - - - +
138C TYR* 3.9 20.0 - - + -
139C HIS* 3.0 18.2 + - - +
140C GLY 3.3 10.2 + - - +
145C THR 2.6 28.2 + - - -
146C LEU* 3.1 20.9 - - - +
147C ALA 3.3 0.5 - - - +
148C LEU* 1.3 73.3 - - - +
150C GLY* 1.3 58.2 + - - +
151C LYS* 3.2 18.9 + - + +
155C TYR* 3.9 17.5 - - + -
168C ARG* 3.3 8.1 + - - -
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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