Contacts of the helix formed by residues 157 - 166 (chain A) in PDB entry 1Z83
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.9 17.5 - - + -
15A GLY 5.6 0.4 - - - +
96A PRO 4.1 11.7 - - - +
97A ARG* 2.8 55.4 + - - +
152A THR 4.3 1.0 + - - -
153A TYR* 3.0 37.3 + - + -
156A ALA* 1.3 76.0 - - - +
158A GLU* 1.3 67.9 + - - +
159A PRO 3.3 1.6 - - - -
160A VAL* 3.0 18.9 + - + +
161A ILE* 3.8 4.0 + - - +
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Residues in contact with GLU 158 (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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117A TYR* 4.3 15.2 + - - +
153A TYR* 3.0 26.6 + - + +
154A TYR* 3.5 44.1 - - - +
157A THR* 1.3 75.1 - - - +
159A PRO* 1.4 63.6 - - + +
161A ILE* 3.1 34.6 + - + +
162A ALA* 3.6 3.5 + - - +
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Residues in contact with PRO 159 (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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99A VAL* 3.8 14.3 - - + +
154A TYR 4.0 3.8 - - - +
155A LYS 3.8 16.8 - - - +
156A ALA 3.6 14.8 - - - +
157A THR 3.4 3.1 - - - -
158A GLU* 1.4 89.9 - - + +
160A VAL* 1.3 58.1 + - - +
161A ILE 3.3 0.2 - - - -
162A ALA* 3.5 10.6 + - + +
163A PHE* 3.1 26.9 + - - +
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Residues in contact with VAL 160 (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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14A VAL* 4.7 9.0 - - + -
96A PRO* 3.9 25.4 - - + +
97A ARG 4.1 3.4 - - - -
98A GLU* 3.5 44.6 - - - +
99A VAL* 3.7 5.8 - - - +
115A LEU* 4.5 8.7 - - + -
156A ALA 4.1 1.6 - - - +
157A THR* 3.0 15.3 + - + +
159A PRO* 1.3 73.3 - - - +
161A ILE* 1.3 65.7 + - - +
163A PHE* 3.2 9.2 + - - +
164A TYR* 3.0 41.8 + - + -
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Residues in contact with ILE 161 (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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14A VAL* 3.4 33.0 - - + -
115A LEU* 3.7 25.8 - - + -
117A TYR* 4.0 43.5 - - + -
153A TYR* 5.0 1.3 - - - +
157A THR 4.3 3.6 - - - +
158A GLU* 3.1 19.9 + - + +
160A VAL* 1.3 76.8 - - - +
162A ALA* 1.3 58.9 + - - +
163A PHE 3.2 0.3 + - - -
164A TYR 3.3 0.5 + - - -
165A GLU* 2.8 34.0 + - + +
170A VAL* 3.9 14.3 - - + +
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Residues in contact with ALA 162 (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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158A GLU 3.6 3.8 + - - +
159A PRO* 3.5 11.3 + - + +
160A VAL 3.4 0.4 - - - -
161A ILE* 1.3 79.8 - - - +
163A PHE* 1.3 62.7 + - - +
165A GLU* 3.5 20.1 + - - +
166A LYS* 3.6 18.9 - - - +
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Residues in contact with PHE 163 (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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99A VAL* 3.9 34.5 - - + -
103A GLU* 4.2 20.9 - - + -
106A GLU* 4.2 2.0 - - - -
159A PRO 3.1 14.7 + - - +
160A VAL* 3.3 11.4 - - - +
161A ILE 3.1 0.4 - - - -
162A ALA* 1.3 80.2 - - - +
164A TYR* 1.3 91.3 + + - +
165A GLU 3.6 0.2 + - - -
166A LYS* 3.6 24.8 + - + +
167A ARG* 3.7 31.9 + - - +
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Residues in contact with TYR 164 (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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12A PHE* 3.7 22.1 - + - -
96A PRO* 4.4 3.6 - - + -
99A VAL* 6.5 0.4 - - - -
102A GLY* 3.4 25.1 + - - -
106A GLU* 3.1 28.1 + - - -
112A PRO* 3.8 15.9 - - + -
115A LEU* 3.7 31.0 - - + -
160A VAL* 3.0 35.9 + - + +
161A ILE 4.2 0.4 - - - +
163A PHE* 1.3 91.8 - + - +
165A GLU* 1.3 66.4 + - - +
166A LYS 3.1 2.5 - - - -
167A ARG* 3.0 48.7 + - - +
168A GLY 3.6 3.5 + - - -
169A ILE* 3.9 17.0 + - + +
170A VAL* 3.9 4.0 - - + -
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Residues in contact with GLU 165 (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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161A ILE* 2.8 26.0 + - + +
162A ALA* 3.5 14.1 - - - +
163A PHE 3.3 0.2 - - - -
164A TYR* 1.3 72.8 - - - +
166A LYS* 1.3 63.2 + - + +
168A GLY* 3.1 17.0 + - - +
170A VAL* 3.6 28.8 - - + +
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Residues in contact with LYS 166 (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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162A ALA* 3.6 18.6 - - - +
163A PHE* 3.6 16.4 - - + +
164A TYR 3.1 0.2 - - - -
165A GLU* 1.3 80.0 - - + +
167A ARG* 1.3 59.5 + - + +
168A GLY 3.7 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