Contacts of the helix formed by residues 288 - 293 (chain G) 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 GLY 288 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120G LYS* 3.9 7.4 - - - -
121G ILE 4.2 6.5 - - - +
286G ASN 3.3 1.4 - - - -
287G LEU* 1.3 81.0 - - - +
289G LEU* 1.3 65.3 + - - +
290G GLU 3.3 2.9 + - - -
291G GLU* 3.4 22.3 + - - +
292G LEU* 3.2 25.8 + - - +
2024G SO4 2.8 15.2 + - - -
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Residues in contact with LEU 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G ILE* 4.5 1.1 - - + -
146G ILE* 4.1 24.2 - - + -
284G THR* 3.8 26.5 - - + +
287G LEU* 4.1 14.8 - - + -
288G GLY* 1.3 75.6 - - - +
290G GLU* 1.3 59.6 + - - +
292G LEU* 3.1 9.9 + - + -
293G GLY 2.8 24.3 + - - -
294G ILE* 2.9 45.2 + - + +
296G LEU* 3.8 29.4 - - + -
302G ILE* 4.0 9.4 - - + -
2024G SO4 2.8 16.0 + - - +
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Residues in contact with GLU 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288G GLY 3.3 0.2 - - - -
289G LEU* 1.3 72.4 - - - +
291G GLU* 1.3 65.6 + - + +
293G GLY* 2.9 20.1 + - - -
294G ILE 5.0 2.5 - - - -
2024G SO4 2.8 23.1 + - - +
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Residues in contact with GLU 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G LYS* 3.2 34.5 + - - -
121G ILE 5.5 1.3 - - - +
288G GLY* 3.4 14.8 - - - +
290G GLU* 1.3 83.2 + - + +
292G LEU* 1.3 60.2 + - + +
293G GLY* 4.6 0.2 - - - -
2024G SO4 3.3 19.3 + - - -
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Residues in contact with LEU 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G ILE* 3.6 45.3 - - + +
123G GLY* 4.5 3.6 - - - +
124G LYS* 4.4 18.6 - - - +
288G GLY 3.2 15.9 + - - +
289G LEU* 3.1 11.5 + - + +
291G GLU* 1.3 79.4 - - + +
293G GLY* 1.3 60.7 + - - +
294G ILE* 3.8 23.1 - - + -
312G ILE* 3.6 35.0 - - + +
315G ILE* 3.9 11.4 - - + -
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Residues in contact with GLY 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289G LEU 2.8 3.6 + - - -
290G GLU* 2.9 12.9 + - - -
291G GLU 3.2 0.2 - - - -
292G LEU* 1.3 81.2 - - - +
294G ILE* 1.3 61.2 + - - +
295G GLU* 3.4 12.1 + - - +
311G LYS* 3.1 31.9 + - - +
312G ILE* 6.2 0.2 - - - -
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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