Contacts of the helix formed by residues 160 - 170 (chain A) in PDB entry 4ZPK
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A LEU* 1.3 75.1 - - - +
161A ASP* 1.3 63.9 + - - +
162A GLN* 3.0 22.6 + - + +
163A GLU* 2.8 53.6 + - + +
164A LEU* 3.0 11.0 + - - +
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Residues in contact with ASP 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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159A LEU 4.6 2.3 - - - +
160A THR* 1.3 76.1 + - - +
162A GLN* 1.3 58.6 + - + +
164A LEU* 3.5 16.7 - - - +
165A LYS* 2.9 27.9 + - - +
85B GLN 4.9 0.9 - - - +
88B ASP* 3.6 24.2 - - + +
89B ASN* 3.0 29.8 + - - -
92B LEU* 3.3 28.3 - - + +
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Residues in contact with GLN 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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160A THR* 3.7 18.9 - - + +
161A ASP* 1.3 76.2 - - + +
163A GLU* 1.3 65.4 + - - +
165A LYS* 3.2 6.5 + - - +
166A HIS* 3.0 28.0 + - + -
79B SER* 4.3 17.4 + - - +
80B GLU* 5.1 6.6 + - - +
82B GLU* 5.4 11.6 - - - +
83B ALA 4.9 6.9 + - - -
85B GLN* 4.4 22.9 + - + +
88B ASP* 3.8 18.9 + - - +
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Residues in contact with GLU 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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158A PHE 4.4 0.2 - - - +
159A LEU* 3.2 21.5 - - + +
160A THR* 2.8 44.0 + - + +
162A GLN* 1.3 74.9 - - + +
164A LEU* 1.3 57.5 + - - +
166A HIS* 3.2 11.8 - - - +
167A LEU* 2.9 24.9 + - - +
67B HIS* 3.3 27.4 + - - -
70B LEU* 3.2 48.5 - - + +
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Residues in contact with LEU 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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159A LEU* 4.6 15.7 - - + +
160A THR 3.0 10.8 + - - +
161A ASP* 3.5 20.9 - - - +
163A GLU* 1.3 73.8 - - - +
165A LYS* 1.3 63.7 + - - +
167A LEU* 3.7 15.7 - - + -
168A ILE* 2.9 52.3 + - + +
88B ASP 4.9 1.1 - - - +
91B TYR* 5.1 1.1 - - + -
92B LEU* 3.7 52.9 - - + +
110B PHE* 5.6 10.1 - - + -
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Residues in contact with LYS 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 ASP 2.9 16.7 + - - +
162A GLN* 3.2 11.4 + - - +
164A LEU* 1.3 80.6 - - - +
166A HIS* 1.3 67.1 + - + +
168A ILE* 3.4 10.3 - - - +
169A LEU* 3.0 26.0 + - + +
188A TYR* 4.6 2.6 + - - -
190A SER* 3.2 25.7 + - - -
191A ASP* 4.2 2.2 + - - -
192A SER* 5.4 1.6 + - - -
82B GLU* 3.8 19.7 + - - +
83B ALA* 3.6 23.7 - - - +
87B MET* 5.7 0.4 - - - +
88B ASP* 3.2 35.2 - - + +
91B TYR* 3.3 33.5 - - + -
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Residues in contact with HIS 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 GLN* 3.0 16.5 + - - +
163A GLU* 3.2 12.8 - - - +
165A LYS* 1.3 82.7 - - + +
167A LEU* 1.3 61.8 + - - +
169A LEU* 3.4 11.4 + - + +
170A GLU* 3.1 23.4 + - - +
70B LEU* 6.0 5.6 - - + +
75B SER* 2.6 45.3 + - - +
79B SER* 4.5 10.5 - - - -
82B GLU* 2.3 39.0 + - - -
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Residues in contact with LEU 167 (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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159A LEU* 4.3 13.9 - - + -
163A GLU 2.9 14.8 + - - +
164A LEU* 3.4 13.5 - - + +
165A LYS 3.1 0.4 - - - -
166A HIS* 1.3 76.5 - - - +
168A ILE* 1.3 58.8 + - + +
170A GLU* 3.0 22.5 + - + +
171A ALA* 3.1 10.2 + - - +
66B THR* 6.1 0.7 - - + -
69B LEU* 6.2 1.8 - - + -
70B LEU* 6.2 4.3 - - + -
99B ILE* 4.2 12.1 - - + -
101B VAL* 3.6 28.9 - - + -
110B PHE* 4.1 20.0 - - + -
223B ILE* 3.7 32.5 - - + +
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Residues in contact with ILE 168 (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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164A LEU* 2.9 42.8 + - + +
165A LYS* 3.4 7.4 - - - +
167A LEU* 1.3 72.0 - - + +
169A LEU* 1.3 64.3 + - - +
171A ALA* 3.5 9.7 - - + +
172A ALA* 3.1 27.4 + - - +
340A ILE* 5.0 5.4 - - + -
91B TYR* 4.0 36.3 - - + +
92B LEU* 5.7 0.4 - - - -
95B LEU* 4.8 9.4 - - + -
99B ILE* 3.6 39.5 - - + -
225B MET* 6.3 2.7 - - + -
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Residues in contact with LEU 169 (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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165A LYS* 3.0 19.6 + - + +
166A HIS* 3.6 10.3 - - + +
168A ILE* 1.3 74.6 - - - +
170A GLU* 1.3 56.8 + - + +
171A ALA 3.0 7.3 + - - -
172A ALA 3.0 29.8 + - - +
173A ASP* 4.2 6.0 + - - +
174A GLY 4.0 19.7 - - - +
192A SER* 4.1 18.6 - - - +
195A PRO* 5.8 5.8 - - + -
196A VAL* 5.4 2.7 - - + -
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Residues in contact with GLU 170 (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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166A HIS 3.1 12.1 + - - +
167A LEU* 3.0 15.9 + - + +
169A LEU* 1.3 74.5 - - + +
171A ALA* 1.3 55.9 + - - +
172A ALA 3.7 0.2 - - - -
73B VAL* 3.6 24.6 - - - +
198B GLN* 3.7 27.7 - - + +
200B ARG* 2.4 56.2 + - + +
223B ILE* 4.0 23.6 - - + +
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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