Contacts of the helix formed by residues 162 - 173 (chain A) in PDB entry 1ZD4
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 GLU 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 6.0 1.9 - - - +
51A THR* 5.1 2.4 - - - +
55A LYS* 2.6 34.5 + - - -
158A MET* 3.9 0.7 - - - -
159A VAL* 2.9 39.9 + - + +
160A LYS 5.1 0.2 - - - -
161A PRO* 1.3 76.2 - - + +
163A PRO* 1.3 67.5 - - + +
164A GLN* 2.8 42.3 + - + +
165A ILE* 3.0 21.7 + - + +
166A TYR* 3.1 1.0 - - - -
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Residues in contact with PRO 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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161A PRO 2.7 10.4 - - - +
162A GLU* 1.3 82.6 - - + +
164A GLN* 1.3 64.1 + - - +
166A TYR* 3.4 14.0 + - + +
167A LYS* 3.3 22.7 + - - +
192A PRO* 4.9 8.7 - - + -
196A LEU* 5.5 9.4 - - + +
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Residues in contact with GLN 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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55A LYS* 4.8 3.6 - - - +
157A GLY 5.4 0.8 + - - -
158A MET* 3.1 34.6 - - + +
162A GLU* 2.8 42.4 + - + +
163A PRO* 1.3 78.0 - - + +
165A ILE* 1.3 64.8 + - - +
167A LYS* 2.7 33.2 + - - +
168A PHE* 3.0 9.2 + - - +
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Residues in contact with ILE 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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122A LEU* 3.7 29.4 - - + -
123A THR 5.7 0.9 - - - +
124A ASN* 5.2 0.9 - - - +
151A ILE* 4.5 5.6 - - + -
153A SER* 4.9 4.9 - - - -
156A VAL* 4.1 14.6 - - + -
158A MET* 3.6 48.0 - - + +
159A VAL* 4.1 16.4 - - - +
160A LYS* 4.2 9.0 - - + +
162A GLU 3.0 20.9 - - - +
164A GLN* 1.3 81.5 - - + +
166A TYR* 1.3 72.4 + - + +
168A PHE* 3.0 8.0 - - + +
169A LEU* 2.9 25.8 + - - +
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Residues in contact with TYR 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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122A LEU* 4.8 7.9 - - + -
160A LYS* 3.4 17.4 - - + +
161A PRO* 3.1 42.3 - - + +
162A GLU 3.1 14.1 - - - -
163A PRO* 3.5 13.7 - - + +
164A GLN 3.0 0.4 - - - -
165A ILE* 1.3 82.5 - - + +
167A LYS* 1.3 65.8 + - - +
169A LEU* 3.1 9.7 + - + +
170A LEU* 3.0 34.9 + - + +
182A PHE* 4.4 12.1 - + - -
189A ASN* 2.9 31.0 + - - -
192A PRO* 3.7 20.4 - - + -
193A ALA* 4.0 16.4 - - + -
196A LEU* 5.2 11.9 - - + -
198A MET* 4.9 8.3 - - + -
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Residues in contact with LYS 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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163A PRO* 3.3 15.2 + - - +
164A GLN* 2.7 16.4 + - - +
166A TYR* 1.3 73.0 - - - +
168A PHE* 1.3 64.7 + - - +
170A LEU* 3.2 11.2 + - + +
171A ASP* 2.9 23.5 + - - +
196A LEU* 3.3 33.8 - - + +
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Residues in contact with PHE 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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151A ILE* 3.6 29.4 - - + -
156A VAL* 3.4 31.4 - - + -
158A MET* 3.5 29.2 - - + -
164A GLN 3.0 5.4 + - - +
165A ILE* 3.0 15.0 - - + +
167A LYS* 1.3 76.4 - - - +
169A LEU* 1.3 49.8 + - - +
171A ASP* 3.2 12.2 + - - +
172A THR* 2.8 55.0 + - + -
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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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7A VAL* 3.8 28.3 - - + -
120A ALA* 4.9 3.1 - - + -
121A ILE 6.2 0.4 - - - +
122A LEU* 3.9 27.8 - - + -
151A ILE* 3.8 25.4 - - + -
165A ILE 2.9 12.2 + - - +
166A TYR* 3.1 14.8 + - + +
168A PHE* 1.3 71.9 - - - +
170A LEU* 1.3 68.8 - - + +
172A THR* 2.9 3.5 + - - -
173A LEU* 2.7 56.6 + - + +
180A VAL* 5.2 0.7 - - + -
182A PHE* 4.7 0.2 - - + -
198A MET* 4.3 22.9 - - + -
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Residues in contact with LEU 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 TYR* 3.0 31.8 + - + +
167A LYS* 3.5 11.9 - - + +
169A LEU* 1.3 82.1 - - + +
171A ASP* 1.3 63.0 + - - +
173A LEU* 3.2 4.1 + - + -
174A LYS* 2.9 18.7 + - - -
175A ALA 3.0 33.7 + - - +
176A SER 3.5 1.6 - - - +
177A PRO* 3.2 43.1 - - + -
180A VAL* 4.3 10.5 - - + -
196A LEU* 5.1 9.0 - - + -
198A MET* 3.9 22.2 - - - -
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Residues in contact with ASP 171 (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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167A LYS 2.9 13.4 + - - +
168A PHE* 3.4 16.4 - - + +
170A LEU* 1.3 76.9 - - - +
172A THR* 1.3 61.6 + - - +
174A LYS* 3.1 20.3 + - - +
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Residues in contact with THR 172 (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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149A PHE* 3.5 48.5 - - + -
151A ILE* 4.2 16.8 - - + -
168A PHE* 2.8 48.0 + - + -
169A LEU 2.9 4.5 + - - -
171A ASP* 1.3 75.0 + - - +
173A LEU* 1.3 62.0 + - + +
174A LYS* 3.1 8.7 + - - +
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Residues in contact with LEU 173 (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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4A ARG* 3.6 8.3 + - - -
5A ALA* 3.8 25.4 - - + -
7A VAL* 3.7 26.2 - - + -
118A THR* 4.5 14.5 - - + +
120A ALA* 4.0 12.6 - - + -
149A PHE* 3.9 26.2 - - + -
169A LEU* 2.7 41.3 + - + +
170A LEU* 3.7 6.7 - - + +
172A THR* 1.3 74.4 - - + +
174A LYS* 1.3 70.8 + - - +
175A ALA* 2.9 14.3 + - + +
180A VAL* 4.1 13.0 - - + -
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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