Contacts of the helix formed by residues 627 - 636 (chain B) in PDB entry 6AHU
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 627 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B GLU* 4.4 13.0 - - - +
204B THR* 4.3 7.6 - - - -
430B ASN* 4.4 17.3 - - - -
432B PHE* 4.3 11.1 - - - -
624B LYS 4.2 0.4 + - - -
625B GLY 3.4 6.9 + - - -
626B TRP* 1.3 75.4 - - - +
628B MET* 1.3 64.6 + - - +
629B ALA* 3.1 3.4 - - - +
630B PHE* 3.2 13.2 + - - +
631B TRP* 3.3 9.0 + - - +
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Residues in contact with MET 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A C 5.7 0.9 - - - +
88A U 3.3 46.2 - - + +
203B GLU* 4.6 11.9 - - - +
204B THR* 4.1 21.1 + - + -
206B ILE* 3.7 26.7 - - + +
207B TRP* 3.5 38.1 - - + +
210B LYS* 6.1 0.7 - - - +
569B ASP* 5.9 0.9 - - - -
627B GLY* 1.3 72.1 - - - +
629B ALA* 1.3 61.4 + - - +
630B PHE 3.2 0.2 - - - -
631B TRP* 3.1 21.2 + - + -
632B ILE* 3.1 28.4 + - + +
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Residues in contact with ALA 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ARG* 3.5 34.8 - - - +
567B ILE* 5.4 2.7 - - + -
569B ASP* 3.5 18.7 - - + +
625B GLY 5.6 1.1 - - - +
626B TRP* 4.0 18.6 - - + -
627B GLY 3.1 5.0 - - - +
628B MET* 1.3 77.5 - - - +
630B PHE* 1.3 64.2 + - - +
632B ILE* 3.9 7.9 - - - +
633B PRO* 3.5 17.3 - - - +
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Residues in contact with PHE 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B PHE* 5.5 2.2 - - + -
509B VAL* 5.6 5.2 - - + -
511B ASP* 3.6 31.0 - - + -
512B PRO* 3.6 20.8 - - + +
513B ARG* 5.0 1.8 - - - -
595B ILE* 3.7 29.2 - - + -
597B ILE* 4.2 15.3 - - + -
620B VAL* 6.1 0.2 - - + -
622B LEU* 3.8 26.2 - - + -
626B TRP* 3.6 42.8 + + + +
627B GLY 3.2 9.5 + - - +
629B ALA* 1.3 81.5 - - - +
631B TRP* 1.3 62.7 + - - +
632B ILE 3.5 0.4 - - - -
633B PRO* 3.3 8.3 - - - +
634B PHE* 3.2 27.5 - - + -
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Residues in contact with TRP 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B THR* 4.1 10.8 - - + +
207B TRP* 3.1 65.3 - + - -
208B HIS* 3.9 10.3 - - - -
244B LEU* 3.6 18.4 - - + -
245B GLN 3.2 35.0 - - - -
246B ASP* 3.8 3.6 - - + -
432B PHE* 3.5 31.8 - + + -
627B GLY 3.3 6.0 + - - +
628B MET* 3.1 23.0 + - + +
630B PHE* 1.3 78.0 - - - +
632B ILE* 1.3 64.8 + - + +
634B PHE* 3.2 23.3 + - - +
635B ILE* 3.4 19.8 - - + +
641B VAL* 3.7 17.9 - - + -
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Residues in contact with ILE 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A C 3.6 26.5 - - - +
88A U 3.3 35.0 - - - +
207B TRP* 4.9 10.5 - - + +
513B ARG* 5.4 2.7 - - + -
516B LEU* 4.9 2.9 - - + -
569B ASP* 5.6 2.7 - - - +
628B MET* 3.1 31.1 + - + +
629B ALA* 3.9 9.9 - - - +
631B TRP* 1.3 75.8 - - + +
633B PRO* 1.4 72.7 - - + +
634B PHE 3.2 0.6 + - - -
635B ILE* 3.4 21.7 + - + -
636B TYR* 3.3 34.8 - - + -
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Residues in contact with PRO 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B ALA* 4.9 9.5 - - + +
512B PRO* 3.8 46.0 - - + +
513B ARG* 4.1 7.4 - - - +
516B LEU* 5.0 10.1 - - + -
517B PRO* 5.4 6.8 - - + +
629B ALA 3.5 15.9 - - - +
630B PHE 3.3 17.7 - - - +
632B ILE* 1.4 91.4 - - + +
634B PHE* 1.3 62.0 + - + +
635B ILE 3.6 0.2 + - - -
636B TYR* 3.9 10.0 + - + +
637B ARG* 3.4 19.4 - - - +
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Residues in contact with PHE 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LEU* 3.7 28.3 - - + -
434B LEU* 4.0 17.9 - - + -
442B ILE* 3.6 49.8 - - + -
443B LEU* 4.4 1.6 - - - -
446B ALA* 4.8 5.8 - - + -
447B ILE* 3.6 30.3 - - + -
512B PRO* 5.5 5.4 - - + -
620B VAL* 5.5 5.8 - - + -
630B PHE* 3.2 31.2 - - + -
631B TRP* 3.2 10.4 + + - +
632B ILE 3.2 1.0 - - - -
633B PRO* 1.3 79.8 - - + +
635B ILE* 1.3 65.4 + - + +
636B TYR 3.3 0.2 - - - -
637B ARG* 3.4 13.6 + - + +
639B VAL* 3.3 21.5 - - + +
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Residues in contact with ILE 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A A 6.2 0.2 - - - +
207B TRP* 3.8 20.9 - - + +
244B LEU* 5.4 1.1 - - + -
520B LYS* 4.7 19.0 - - - +
521B SER* 4.2 5.4 + - - -
631B TRP* 3.4 46.2 - - + +
632B ILE* 3.4 22.4 + - + +
633B PRO 3.3 0.8 - - - -
634B PHE* 1.3 82.2 - - + +
636B TYR* 1.3 62.4 + - + +
637B ARG 3.2 4.0 + - - -
638B GLY* 3.7 7.8 + - - -
639B VAL* 4.2 17.5 + - + +
641B VAL* 4.1 16.6 - - + -
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Residues in contact with TYR 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A A 3.7 5.5 + - - -
87A C 3.2 51.9 + - - -
261A G 5.5 3.2 + - - -
516B LEU* 4.6 10.3 - - + -
517B PRO* 4.3 21.1 - - + +
518B GLN 4.8 5.6 - - - -
519B LYS 3.5 21.9 - - - +
520B LYS* 3.7 30.1 - - + -
521B SER 3.4 8.4 + - - +
522B LYS* 3.0 23.9 + - - +
632B ILE* 3.3 43.7 - - + -
633B PRO* 3.9 6.3 + - + +
634B PHE 3.3 0.8 - - - -
635B ILE* 1.3 79.6 - - + +
637B ARG* 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