Contacts of the helix formed by residues 145 - 153 (chain C) in PDB entry 6UZA
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 HIS 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106C ALA 3.6 14.4 - - - -
107C GLU 3.0 27.6 + - - -
108C TYR 4.3 0.2 - - - -
109C GLY* 3.5 23.6 + - - -
140C ALA* 3.0 13.2 + - + +
143C ASN* 3.7 17.2 - - + +
144C GLU* 1.3 77.7 + - - +
146C LEU* 1.3 56.5 + - - +
147C GLU* 3.3 7.2 + - - +
148C ILE* 4.1 22.4 - - + -
149C THR* 2.7 35.7 + - - -
176C ILE* 4.1 1.5 - - - +
889C GLN* 3.6 42.4 + - + -
890C ASP* 5.7 0.6 + - - -
893C SER* 4.2 8.2 - - - -
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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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144C GLU* 3.8 12.8 + - - +
145C HIS* 1.3 71.8 - - - +
147C GLU* 1.3 74.6 + - + +
149C THR* 3.4 5.0 + - - -
150C GLU* 2.9 42.3 + - + +
175C ARG* 3.5 74.9 - - + +
176C ILE* 4.3 13.4 - - + +
179C ALA* 4.1 16.4 - - + -
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Residues in contact with GLU 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 ILE* 3.3 34.3 - - + +
145C HIS* 4.9 5.2 + - - +
146C LEU* 1.3 92.2 + - + +
148C ILE* 1.3 60.9 + - - +
150C GLU* 3.5 9.3 + - - +
151C LEU* 2.9 30.2 + - - +
893C SER* 3.8 9.4 + - - -
897C GLU* 5.2 0.2 - - - +
895D ARG* 3.7 38.4 + - - +
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Residues in contact with ILE 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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105C ALA 3.6 23.6 - - - +
106C ALA* 3.9 16.2 - - - +
109C GLY* 3.7 25.8 - - - -
110C ASN 4.2 1.6 - - - +
111C ILE* 3.8 23.8 - - + +
114C VAL* 4.3 17.0 - - + -
140C ALA* 3.9 11.0 - - + -
145C HIS* 3.7 18.5 + - + -
146C LEU 3.4 0.2 - - - -
147C GLU* 1.3 74.2 - - - +
149C THR* 1.3 59.3 + - - +
151C LEU* 3.6 7.3 - - - +
152C LEU* 2.9 47.3 + - + +
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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
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137C LEU* 4.1 19.7 - - + -
140C ALA* 3.8 17.1 + - - +
141C VAL* 4.0 16.6 - - + +
145C HIS 2.7 23.9 + - - -
146C LEU* 3.6 8.2 - - - -
147C GLU 3.3 0.2 - - - -
148C ILE* 1.3 76.3 - - - +
150C GLU* 1.3 57.6 + - - +
152C LEU* 3.3 1.4 + - - +
153C LEU* 2.9 48.8 + - + +
176C ILE* 4.4 10.1 - - + +
179C ALA* 5.2 5.6 - - + -
180C ILE* 4.3 8.5 - - + -
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Residues in contact with GLU 150 (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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146C LEU* 2.9 37.0 + - + +
147C GLU* 4.0 6.9 - - - +
149C THR* 1.3 74.4 - - - +
151C LEU* 1.3 59.3 + - - +
152C LEU 3.5 0.2 - - - -
153C LEU* 4.1 9.1 + - + +
154C LYS* 3.3 28.4 + - - +
179C ALA* 4.0 26.7 - - + +
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Residues in contact with LEU 151 (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 ILE* 4.3 16.8 - - + +
114C VAL* 3.7 26.2 - - + -
115C ARG* 3.7 38.4 - - + +
118C LEU* 3.5 23.0 - - + +
147C GLU 2.9 16.7 + - - +
148C ILE* 3.6 6.7 - - - +
149C THR 3.2 0.2 - - - -
150C GLU* 1.3 79.5 - - - +
152C LEU* 1.3 60.1 + - - +
153C LEU 3.5 0.2 - - - -
154C LYS* 4.0 28.3 + - - +
155C LYS* 5.6 0.9 - - - +
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Residues in contact with LEU 152 (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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102C PHE* 3.9 26.2 - - + -
106C ALA* 5.1 0.7 - - + -
114C VAL* 5.0 2.7 - - + -
118C LEU* 4.1 18.4 - - + -
126C VAL* 4.9 4.0 - - + -
136C ALA* 3.9 34.8 - - + +
137C LEU* 4.2 10.1 - - + +
140C ALA* 4.7 1.6 - - + -
148C ILE* 2.9 38.6 + - + +
149C THR 3.3 2.7 + - - +
151C LEU* 1.3 73.5 - - - +
153C LEU* 1.3 62.2 + - - +
154C LYS 3.1 6.6 + - - -
155C LYS* 3.3 17.6 - - + +
158C LEU* 3.3 36.7 - - + +
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Residues in contact with LEU 153 (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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137C LEU* 4.5 8.5 - - + -
149C THR* 2.9 40.2 + - + +
150C GLU* 4.1 7.1 + - + +
151C LEU 3.5 0.6 - - - -
152C LEU* 1.3 75.1 - - - +
154C LYS* 1.3 57.9 + - + +
155C LYS 3.3 4.8 + - - -
156C GLU 4.7 1.2 + - - -
158C LEU* 4.1 14.6 - - + -
161C VAL* 4.2 21.1 - - + -
179C ALA* 3.5 28.0 - - + +
180C ILE* 3.9 13.5 - - + -
183C HIS* 3.8 43.8 + - + +
184C PRO* 5.7 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