Contacts of the helix formed by residues 288 - 295 (chain D) in PDB entry 3HB1
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D SER 3.3 7.9 + - - -
285D LEU 4.2 4.9 + - - -
286D LEU 3.3 4.0 + - - -
287D THR* 1.3 78.7 + - - +
289D THR* 1.3 63.7 + - - +
290D PHE 3.0 4.5 + - - -
291D ALA* 3.2 10.9 + - - +
292D SER* 3.1 22.6 + - - -
298D THR* 5.6 3.6 - - - +
301D SER* 6.0 0.9 - - - -
302D VAL* 6.2 1.3 - - - -
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Residues in contact with THR 289 (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 SER* 3.5 12.1 - - - -
287D THR* 3.2 22.7 + - - +
288D GLY* 1.3 76.8 - - - +
290D PHE* 1.3 60.9 + - - +
292D SER* 3.1 9.1 + - - -
293D ARG* 3.0 51.7 + - - +
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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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281D ILE* 3.9 26.5 - - + -
284D SER* 3.2 32.4 + - - +
285D LEU* 3.8 17.7 - - + -
288D GLY 3.0 1.0 + - - -
289D THR* 1.3 82.3 + - - +
291D ALA* 1.3 72.0 + - - +
292D SER 3.1 0.2 + - - -
293D ARG* 4.5 2.7 - - - +
294D TYR* 2.9 67.7 + + + +
296D LYS* 4.0 12.1 - - + -
301D SER* 3.9 4.5 - - - -
420D LEU* 3.7 41.7 - - + -
421D THR* 3.8 18.6 - - + -
424D TRP* 5.2 3.1 - + - -
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Residues in contact with ALA 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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284D SER 4.5 0.2 + - - -
288D GLY* 3.2 9.1 + - - +
290D PHE* 1.3 86.9 - - - +
292D SER* 1.3 57.4 + - - +
295D GLY* 2.9 24.9 + - - -
296D LYS* 2.9 24.1 + - - +
298D THR* 3.6 32.1 - - + -
301D SER* 3.4 22.6 + - - +
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Residues in contact with SER 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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288D GLY 3.1 9.4 + - - -
289D THR* 3.1 19.8 + - - -
291D ALA* 1.3 81.4 - - - +
293D ARG* 1.3 71.5 + - - +
294D TYR 3.2 1.0 + - - -
295D GLY* 3.4 7.8 + - - -
298D THR* 5.1 5.3 - - - +
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Residues in contact with ARG 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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277D GLU* 5.0 7.7 - - - +
281D ILE* 6.2 1.2 - - - +
284D SER* 4.5 7.7 + - - -
289D THR* 3.0 41.8 + - - +
290D PHE* 4.0 4.5 - - - +
292D SER* 1.3 82.5 + - - +
294D TYR* 1.3 93.2 + - + +
424D TRP* 5.9 1.6 - - - -
521D SER 3.3 24.9 + - - -
522D CYS* 5.9 2.2 - - + -
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Residues in contact with TYR 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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281D ILE* 5.6 0.4 - - + -
290D PHE* 2.9 54.1 + + + +
293D ARG* 1.3 114.3 + - + +
295D GLY* 1.3 67.8 + - - +
296D LYS* 3.4 25.5 + - + +
422D ASP* 6.1 0.9 - - - +
424D TRP* 3.7 12.6 - + - -
522D CYS* 3.2 18.4 - - + +
523D HIS* 3.2 41.2 + + + -
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Residues in contact with GLY 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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291D ALA 2.9 9.7 + - - -
292D SER 3.4 7.9 + - - -
293D ARG 3.6 0.2 - - - -
294D TYR* 1.3 80.0 - - - +
296D LYS* 1.3 63.1 + - - +
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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