Contacts of the helix formed by residues 167 - 173 (chain D) in PDB entry 1ZMD
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 SER 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D VAL* 3.8 32.7 - - - +
160D ILE* 3.7 12.6 - - - +
162D GLU* 2.8 30.3 + - - -
166D VAL* 1.3 74.4 - - - +
168D SER* 1.3 66.7 + - - +
169D THR* 3.0 14.4 + - - -
170D GLY 3.2 0.7 + - - -
171D ALA* 3.0 19.8 + - - +
275D LEU* 3.6 4.5 - - - -
276D VAL 3.7 9.6 - - - -
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Residues in contact with SER 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D VAL 4.6 0.7 + - - -
152D VAL* 4.4 10.4 - - - +
167D SER* 1.3 75.1 + - - +
169D THR* 1.3 61.4 + - - +
171D ALA* 3.7 1.2 - - - +
172D LEU* 2.9 36.5 + - - +
189D ILE* 4.1 15.6 - - - +
193D LEU* 3.7 20.6 - - - +
275D LEU* 3.8 5.2 - - - +
276D VAL 4.5 2.0 + - - -
277D CYS* 5.5 1.2 - - - +
280D ARG* 4.4 0.5 + - - -
480D FAD 3.7 39.7 - - - +
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Residues in contact with THR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D VAL* 3.5 40.0 - - + +
152D VAL* 5.3 3.8 - - - +
162D GLU* 4.0 9.2 - - + +
167D SER* 3.0 12.8 + - - -
168D SER* 1.3 81.5 + - - +
170D GLY* 1.3 64.0 + - - +
172D LEU* 3.0 23.2 + - - +
173D SER* 3.5 8.5 + - - -
280D ARG* 5.9 0.7 + - - -
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Residues in contact with GLY 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D GLU* 3.2 33.5 + - - +
166D VAL* 4.0 9.0 - - - -
167D SER 3.2 4.0 + - - -
169D THR* 1.3 80.0 - - - +
171D ALA* 1.3 63.2 + - - +
173D SER* 2.9 16.0 + - - -
174D LEU* 3.1 18.2 + - - +
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Residues in contact with ALA 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 5.0 0.2 - - - +
166D VAL* 3.7 18.1 - - + +
167D SER 3.0 16.0 + - - +
168D SER 3.7 4.7 - - - +
170D GLY* 1.3 76.7 - - - +
172D LEU* 1.3 60.1 - - - +
173D SER 3.4 0.7 + - - -
174D LEU* 3.7 9.5 - - + +
181D MET* 5.8 1.6 - - - -
193D LEU* 4.0 13.4 - - + +
197D TRP* 3.0 39.0 + - + +
275D LEU* 3.9 18.4 - - + -
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D VAL* 3.3 38.8 - - - +
49D GLY 4.4 0.2 - - - +
52D PRO* 3.7 20.0 - - + +
53D SER* 3.7 31.0 - - - +
56D LEU* 3.6 16.0 - - + +
89D MET* 3.1 13.4 - - - +
92D LYS* 2.9 21.3 + - - +
168D SER 2.9 22.7 + - - +
169D THR* 3.4 10.1 - - + +
170D GLY 3.0 0.8 - - - -
171D ALA* 1.3 79.4 - - - +
173D SER* 1.3 59.0 + - - +
174D LEU 3.8 0.4 - - - -
193D LEU* 3.8 21.5 - - + -
480D FAD 4.4 6.3 - - + -
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Residues in contact with SER 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D MET* 3.7 8.2 - - - +
92D LYS* 2.9 20.9 + - - +
169D THR 3.5 7.6 + - - -
170D GLY* 2.9 9.9 + - - -
172D LEU* 1.3 78.9 - - - +
174D LEU* 1.3 67.9 + - - +
175D LYS* 3.2 21.7 + - - +
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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