Contacts of the helix formed by residues 284 - 292 (chain D) in PDB entry 3ZNG
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 PRO 284 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283D LEU* 1.3 95.1 - - + +
285D GLU* 1.3 65.1 + - - +
286D ASP* 3.1 22.9 - - - +
287D LEU* 3.0 23.1 + - + +
288D LYS* 3.1 10.4 + - - +
105E MET* 4.0 21.3 - - + -
108E ASN* 6.2 0.7 - - - +
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Residues in contact with GLU 285 (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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283D LEU 3.6 2.2 + - - -
284D PRO* 1.3 71.4 - - - +
286D ASP* 1.3 62.3 + - - +
288D LYS* 3.8 31.2 + - - +
289D GLN* 3.1 53.2 + - - +
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Residues in contact with ASP 286 (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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284D PRO* 3.1 22.5 - - - +
285D GLU* 1.3 78.6 - - - +
287D LEU* 1.3 86.5 + - - +
289D GLN* 3.9 8.8 - - - +
290D PHE* 3.1 24.1 + - - +
108E ASN* 3.7 17.8 + - - -
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Residues in contact with LEU 287 (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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259D MET* 5.0 2.9 - - - -
283D LEU* 4.0 17.7 - - + -
284D PRO* 3.0 12.9 + - + +
286D ASP* 1.3 99.7 + - - +
288D LYS* 1.3 60.1 + - - +
289D GLN 3.1 1.1 - - - -
290D PHE* 3.5 13.5 - - + +
291D LEU* 2.8 36.3 + - - +
104E LEU* 4.0 33.4 - - + -
105E MET* 3.7 35.0 - - + -
108E ASN* 4.0 27.4 - - + +
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Residues in contact with LYS 288 (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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278D ILE* 3.9 25.0 - - + +
279D THR* 3.0 31.4 + - + +
281D LEU 3.2 22.1 + - - -
283D LEU* 3.1 33.1 + - + +
284D PRO 3.1 10.7 + - - +
285D GLU* 3.3 32.4 + - - +
287D LEU* 1.3 75.9 - - - +
289D GLN* 1.3 57.6 + - - +
291D LEU* 3.5 4.0 + - - +
292D LEU* 3.1 38.2 + - + +
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Residues in contact with GLN 289 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285D GLU* 3.1 46.6 + - - +
286D ASP* 3.9 7.0 - - - +
288D LYS* 1.3 74.5 - - - +
290D PHE* 1.3 62.9 + - - +
292D LEU* 3.4 4.4 + - + +
293D HIS 3.1 3.5 + - - -
294D LEU* 2.9 60.0 + - + +
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Residues in contact with PHE 290 (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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259D MET* 3.6 49.4 - - + -
260D GLN* 4.4 5.2 - - + -
263D ARG* 3.0 68.8 + - + -
286D ASP 3.1 19.0 + - - +
287D LEU* 3.2 17.0 + - + +
289D GLN* 1.3 76.5 - - - +
291D LEU* 1.3 65.0 + - + +
293D HIS* 3.2 7.7 + - - +
294D LEU 5.1 0.9 - - - +
104E LEU* 4.0 12.6 - - + -
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Residues in contact with LEU 291 (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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263D ARG* 3.8 34.7 - - + +
266D ILE* 4.0 28.5 - - + -
267D ARG* 2.8 39.1 + - + +
278D ILE* 3.7 28.1 - - + +
281D LEU* 4.5 4.0 - - + -
283D LEU* 3.8 28.7 - - + -
287D LEU 2.8 19.9 + - - +
288D LYS 3.8 2.9 - - - +
290D PHE* 1.3 74.2 - - + +
292D LEU* 1.3 52.1 + - - +
293D HIS* 3.8 2.1 + - - -
101E LEU* 4.9 0.2 - - + -
104E LEU* 3.7 24.0 - - + -
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Residues in contact with LEU 292 (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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188D GLU* 4.8 8.5 - - - +
267D ARG* 4.0 5.5 + - - +
275D HIS* 3.4 34.1 - - + +
276D HIS* 4.5 7.4 - - - +
278D ILE* 4.2 19.7 - - + -
279D THR* 4.8 12.1 - - - +
288D LYS* 3.1 24.0 + - + +
289D GLN* 3.4 1.3 + - + +
290D PHE 3.2 0.6 - - - -
291D LEU* 1.3 77.2 - - - +
293D HIS* 1.3 71.6 + - - +
294D LEU* 3.7 32.1 + - + +
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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