Contacts of the helix formed by residues 377 - 386 (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 ILE 377 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D ASP* 3.0 20.2 + - - +
210D LEU* 4.7 1.3 - - + -
248D SER* 3.7 44.2 - - - +
251D THR* 4.1 20.0 - - + +
252D LEU* 4.3 7.4 - - - +
255D ARG* 3.2 27.8 - - - +
371D VAL* 3.9 17.3 - - + -
376D GLY* 1.3 75.5 - - - -
378D ASP* 1.3 66.5 + - - +
379D PRO 3.5 0.4 - - - -
380D ILE* 3.4 2.9 + - - +
381D LEU* 2.9 50.2 + - + +
541D THR* 4.3 3.8 - - + -
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Residues in contact with ASP 378 (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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205D ASP* 4.4 4.3 + - - +
206D ASN* 5.0 11.6 + - - +
208D ARG* 5.4 0.3 + - - -
255D ARG* 4.7 1.0 + - - -
375D GLY 4.4 2.2 + - - +
377D ILE* 1.3 82.0 - - - +
379D PRO* 1.4 70.4 - - + +
382D ARG* 3.0 37.6 + - - +
541D THR* 3.2 25.6 - - - +
542D GLY* 3.0 29.8 + - - -
543D ILE* 3.5 26.5 + - + +
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Residues in contact with PRO 379 (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 16.4 - - + -
346D LEU 3.1 33.7 + - - +
347D ASP* 5.7 0.2 - - - -
353D MET* 3.8 32.1 - - + -
374D GLU 5.0 1.3 - - - +
375D GLY* 3.4 28.0 - - - +
376D GLY 3.9 3.8 - - - +
377D ILE 3.8 1.3 - - - -
378D ASP* 1.4 94.7 - - + +
380D ILE* 1.3 57.0 + - + +
382D ARG* 3.9 10.5 - - - +
383D GLY 3.1 14.9 + - - -
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Residues in contact with ILE 380 (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* 3.7 22.9 - - + +
245D GLU* 3.4 35.0 - - + +
248D SER* 3.2 28.9 - - - +
343D MET* 4.5 5.8 - - + -
344D PHE 4.2 2.7 - - - +
345D ARG* 4.1 24.2 - - + -
370D ARG 5.5 1.6 - - - +
371D VAL* 4.1 13.9 - - + +
376D GLY 3.5 20.0 - - - +
377D ILE* 3.6 2.9 - - - +
378D ASP 3.2 0.6 - - - -
379D PRO* 1.3 73.5 - - + +
381D LEU* 1.4 65.8 + - - +
383D GLY* 3.0 11.8 + - - -
384D LEU* 3.0 15.8 + - + +
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Residues in contact with LEU 381 (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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85B MET* 4.2 8.9 - - + +
248D SER* 4.0 18.6 - - - +
249D MET* 3.7 30.3 - - - -
252D LEU* 4.2 13.5 - - + -
377D ILE* 2.9 39.1 + - + +
380D ILE* 1.4 72.0 - - - +
382D ARG* 1.3 63.4 + - - +
384D LEU* 3.2 9.1 + - + +
385D MET* 3.1 33.6 + - + +
537D ILE* 4.4 9.4 - - + -
541D THR* 3.7 30.3 - - + -
543D ILE* 3.9 11.7 - - + -
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Residues in contact with ARG 382 (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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346D LEU* 2.6 39.3 + - + +
347D ASP* 2.9 29.1 + - - +
348D ASN* 3.2 21.0 - - - +
350D TYR* 3.6 36.2 - - + +
378D ASP* 3.0 22.8 + - - +
379D PRO* 3.9 19.6 - - - +
381D LEU* 1.3 75.9 - - - +
383D GLY* 1.4 56.5 + - - +
385D MET* 3.2 9.4 + - - +
386D ALA* 2.9 32.7 + - - +
542D GLY 5.4 1.0 + - - -
543D ILE* 3.5 28.9 - - + +
758D BR 3.7 12.5 - - - +
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Residues in contact with GLY 383 (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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84B LEU* 4.4 2.4 - - - +
344D PHE* 3.1 31.6 - - - -
346D LEU* 4.1 11.4 - - - +
379D PRO 3.1 8.8 + - - -
380D ILE 3.0 4.9 + - - -
382D ARG* 1.4 76.3 - - - +
384D LEU* 1.3 61.5 + - - +
387D THR* 2.9 33.7 + - - -
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Residues in contact with LEU 384 (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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83B SER* 3.4 3.1 - - - -
84B LEU* 3.2 39.2 + - + +
85B MET* 3.1 51.4 + - + +
87B MET* 5.3 0.9 - - + -
88B GLN* 3.9 32.8 - - + +
245D GLU* 3.8 38.4 - - + +
249D MET* 4.4 5.2 - - - -
380D ILE* 3.0 19.0 + - + +
381D LEU* 3.2 12.1 + - + +
383D GLY* 1.3 75.6 - - - +
385D MET* 1.3 61.9 + - - +
387D THR 3.8 0.5 - - - +
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Residues in contact with MET 385 (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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83B SER* 3.9 3.5 - - - -
85B MET* 4.5 7.2 - - + -
350D TYR* 3.6 18.6 - - - +
381D LEU* 3.1 32.1 + - + +
382D ARG* 3.2 7.8 + - - +
384D LEU* 1.3 81.4 - - - +
386D ALA* 1.3 58.0 + - - +
387D THR 3.4 0.8 + - - -
537D ILE* 4.0 28.0 - - + -
543D ILE* 4.2 16.6 - - + -
546D VAL* 4.3 5.2 - - + -
547D SER* 3.1 39.7 + - - +
551D ILE* 4.2 16.6 - - + -
554D SER 3.8 5.4 - - - +
555D ASN* 3.1 23.4 - - - -
561D PHE* 3.8 11.1 - - + -
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Residues in contact with ALA 386 (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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346D LEU* 3.6 26.4 - - + +
350D TYR* 3.6 20.0 - - + -
382D ARG 2.9 5.8 + - - +
384D LEU 3.5 0.2 - - - -
385D MET* 1.3 75.0 - - - +
387D THR* 1.3 62.1 + - - +
388D PRO* 4.4 1.2 - - - +
555D ASN 3.2 17.4 - - - +
556D SER* 5.1 0.7 - - - -
557D TYR* 4.2 11.7 + - + +
561D PHE* 3.8 10.1 - - + -
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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