Contacts of the helix formed by residues 292 - 300 (chain D) in PDB entry 5M8N
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 292 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290D CYS 3.6 1.6 - - - -
291D ASP* 1.3 73.4 - - - +
293D LEU* 1.3 63.7 + - - +
294D GLU* 3.3 3.4 - - - +
295D ASP* 3.0 34.6 + - - +
296D TYR* 3.2 16.2 + - - -
308D ASP* 4.8 4.3 + - - -
1R NAG 3.4 22.0 - - - -
2R NAG 3.7 23.9 + - - +
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Residues in contact with LEU 293 (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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193D TYR* 5.6 2.2 - - + -
198D LYS* 5.1 7.4 - - - +
290D CYS 3.6 5.2 - - - +
291D ASP 3.1 22.4 + - - +
292D SER* 1.3 69.6 - - - +
294D GLU* 1.3 53.9 + - - +
295D ASP 2.8 7.4 + - - -
296D TYR* 2.6 38.4 + - + -
297D ASP* 2.8 35.3 + - - +
392D HIS* 3.0 56.5 - - + +
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Residues in contact with GLU 294 (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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292D SER* 3.3 1.1 - - - -
293D LEU* 1.3 76.9 - - - +
295D ASP* 1.3 55.3 + - - +
297D ASP* 5.2 2.0 - - - -
298D THR* 2.5 43.9 + - + +
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Residues in contact with ASP 295 (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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292D SER* 3.2 32.7 + - - +
293D LEU 2.8 1.4 + - - -
294D GLU* 1.3 83.4 - - - +
296D TYR* 1.3 59.1 + - + +
298D THR* 3.8 1.6 - - - -
299D LEU* 2.9 40.8 + - + +
301D THR* 3.0 11.2 + - + +
1R NAG 3.7 15.7 - - - +
2R NAG 3.2 40.1 + - - +
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Residues in contact with TYR 296 (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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193D TYR* 3.5 30.7 - + - +
197D LYS* 5.2 4.0 - - - -
200D PHE* 4.5 1.9 - - - +
290D CYS* 3.2 33.7 + - - -
291D ASP 3.7 0.5 + - - -
292D SER* 3.2 22.1 + - - -
293D LEU* 2.6 24.6 + - + +
295D ASP* 1.3 71.5 - - - +
297D ASP* 1.3 64.3 + - - +
300D GLY* 2.9 27.4 + - - -
301D THR* 3.0 32.9 + - - +
302D LEU 4.0 2.9 - - - -
303D CYS* 3.5 38.5 - - + -
304D ASN* 4.5 2.9 + - - -
1R NAG 3.0 26.3 + - - -
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Residues in contact with ASP 297 (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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193D TYR* 5.9 0.3 - - - -
197D LYS* 4.9 5.9 - - - +
198D LYS* 3.0 53.9 + - - +
200D PHE* 3.7 6.1 - - - -
205D GLN 4.2 4.9 - - - +
207D SER* 2.5 36.7 + - - +
293D LEU* 2.8 35.7 + - - +
294D GLU* 5.2 0.7 - - - -
296D TYR* 1.3 81.8 - - - +
298D THR* 1.3 64.8 + - + +
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Residues in contact with THR 298 (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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200D PHE* 3.5 11.6 - - - -
202D GLY 4.4 0.5 - - - +
203D VAL* 4.0 13.9 - - - +
204D GLY 4.4 4.4 + - - +
205D GLN 5.5 2.2 - - - -
294D GLU* 2.5 45.1 + - + +
295D ASP* 3.5 3.5 + - - -
297D ASP* 1.3 83.9 - - + +
299D LEU* 1.3 73.2 + - - +
300D GLY 3.3 1.6 - - - -
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Residues in contact with LEU 299 (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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168D GLU* 4.6 7.4 - - - +
200D PHE* 3.7 9.5 - - - -
203D VAL* 4.8 14.5 - - + +
295D ASP* 2.9 30.7 + - + +
298D THR* 1.3 87.5 + - - +
300D GLY* 1.3 61.4 + - - +
301D THR* 3.5 21.2 + - + +
2R NAG 3.9 21.5 - - - +
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Residues in contact with GLY 300 (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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165D ARG* 2.6 30.8 + - - +
168D GLU* 4.1 6.4 - - - +
197D LYS* 6.1 0.2 - - - -
200D PHE* 3.3 37.6 - - - -
296D TYR 2.9 11.5 + - - -
299D LEU* 1.3 79.0 - - - +
301D THR* 1.3 62.3 + - - +
302D LEU* 4.1 0.3 - - - +
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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