Contacts of the helix formed by residues 368 - 374 (chain D) in PDB entry 1D7W
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 368 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221D CYS* 3.3 22.2 + - - +
224D THR* 4.5 0.2 + - - -
230D ILE* 3.4 10.6 + - - +
231D PRO 2.9 27.2 + - - -
233D PHE* 3.6 26.0 - - - -
241D SER* 4.4 4.2 + - - +
244D PRO* 6.0 0.2 - - - -
247D THR* 5.8 1.1 - - - -
366D PHE 2.8 9.3 + - - -
367D ALA* 1.3 71.1 - - - +
369D TRP* 1.3 63.1 + - - +
371D VAL* 3.0 20.7 + - - +
372D VAL* 3.5 11.8 + - - +
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Residues in contact with TRP 369 (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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221D CYS 5.2 0.9 - - - -
224D THR* 3.4 28.7 + - - -
225D ASN* 3.4 30.9 - - + +
228D ALA* 3.8 8.3 - - + -
230D ILE* 3.5 34.1 - - + +
367D ALA* 3.1 18.5 - - + +
368D SER* 1.3 80.2 + - - +
370D ARG* 1.3 87.9 + - + +
371D VAL 3.3 0.2 - - - -
372D VAL* 4.5 0.4 - - - -
373D LEU* 2.8 45.3 + - + +
374D GLU* 3.5 28.7 - - + -
2630D NAG 3.3 51.8 - - + -
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Residues in contact with ARG 370 (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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244D PRO* 4.7 7.2 - - + -
343D MET* 4.2 17.9 - - + -
345D ARG* 4.2 6.5 + - - +
356D ASN* 5.8 1.6 - - - +
359D VAL* 3.5 36.2 - - - +
363D ARG* 2.9 41.0 + - - +
364D VAL* 4.2 4.0 - - - +
367D ALA* 2.9 23.8 + - - +
369D TRP* 1.3 111.8 - - + +
371D VAL* 1.3 57.1 + - - +
374D GLU* 3.0 72.1 + - + +
376D GLY 4.7 1.0 + - - +
380D ILE* 5.5 2.4 - - + +
409D GLN* 5.7 0.4 - - - +
2630D NAG 5.2 2.2 + - - -
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Residues in contact with VAL 371 (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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210D LEU* 4.0 19.7 - - + +
233D PHE* 4.4 11.2 - - + -
244D PRO* 4.2 22.7 - - + +
247D THR* 4.3 18.2 - - + +
248D SER* 5.0 0.2 - - - +
367D ALA 4.9 0.4 - - - +
368D SER* 3.0 13.9 + - - +
370D ARG* 1.3 77.1 - - - +
372D VAL* 1.3 59.5 - - - +
376D GLY* 2.9 42.4 + - - -
377D ILE* 3.9 25.4 - - + -
380D ILE* 4.1 19.3 - - + -
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Residues in contact with VAL 372 (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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203D PHE* 3.6 40.4 - - + +
204D GLN 5.3 4.5 - - - +
210D LEU* 4.2 17.1 - - + +
213D PHE* 4.0 8.1 - - + -
230D ILE* 3.8 33.4 - - + -
233D PHE* 3.6 28.3 - - + -
368D SER 3.5 1.8 + - - +
369D TRP 3.9 4.9 - - - +
371D VAL* 1.3 77.0 - - - +
373D LEU* 1.4 64.2 + - + +
375D GLY 5.2 0.9 + - - -
376D GLY 5.3 0.5 + - - -
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Residues in contact with LEU 373 (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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203D PHE* 5.2 7.9 - - + -
228D ALA* 3.8 19.5 - - + +
230D ILE* 4.5 7.6 - - + -
369D TRP* 2.8 30.4 + - + +
372D VAL* 1.4 87.8 - - + +
374D GLU* 1.3 63.4 + - + +
375D GLY 3.6 2.8 + - - -
2630D NAG 3.2 36.3 - - - +
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Residues in contact with GLU 374 (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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345D ARG* 3.3 35.1 + - - +
353D MET* 4.1 20.0 - - + +
355D PRO* 6.0 1.2 - - - +
356D ASN* 4.5 12.3 + - - -
369D TRP* 3.5 22.6 - - + -
370D ARG* 3.0 62.1 + - - +
372D VAL 3.7 0.2 - - - -
373D LEU* 1.3 82.5 - - + +
375D GLY* 1.3 56.7 + - - +
376D GLY 3.6 3.4 + - - +
379D PRO* 4.7 2.1 - - - +
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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