Contacts of the helix formed by residues 677 - 682 (chain A) in PDB entry 5M7R
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 GLU 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676A GLN* 1.4 76.9 + - - +
678A PRO* 1.4 89.2 - - + +
679A TRP* 3.1 4.8 + - - +
680A ALA* 3.6 9.4 + - - +
681A PHE* 4.6 0.9 - - - -
711A THR* 3.6 33.7 + - - +
712A SER* 3.1 34.7 + - - +
714A VAL* 3.5 12.9 - - - +
222B THR* 4.3 2.1 + - + -
253B LYS* 3.7 39.2 - - + +
254B VAL* 4.1 4.3 + - - +
255B VAL 4.0 10.2 + - - -
569B TYR* 3.6 17.4 + - - -
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Residues in contact with PRO 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A GLU* 1.4 105.0 - - + +
679A TRP* 1.3 62.6 + - + +
681A PHE* 2.9 27.3 + - + +
682A ARG* 3.5 8.9 + - - +
711A THR 5.1 1.1 - - - +
714A VAL* 4.5 11.2 - - + -
255B VAL* 4.5 7.9 - - + -
286B TYR* 3.5 43.7 - - + +
287B ASP* 5.4 1.3 - - - +
290B ARG* 3.9 10.0 + - - +
568B PRO* 6.2 0.4 - - + -
569B TYR* 3.5 14.6 - - + +
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Residues in contact with TRP 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A SER* 5.1 6.7 + - - -
650A ILE* 4.1 18.4 - - + -
653A MET* 3.7 42.0 - - + +
672A LEU* 5.0 20.6 - - + -
677A GLU* 3.1 3.0 + - - +
678A PRO* 1.3 79.9 - - + +
680A ALA* 1.3 64.5 + - - +
681A PHE 3.2 0.2 - - - -
682A ARG* 3.3 50.9 + - + +
710A PRO 5.3 2.7 - - - -
711A THR* 5.3 13.0 + - - +
713A LYS 6.2 0.4 - - - -
690B GLN* 3.9 31.9 - - + -
693B LEU* 4.0 28.9 - - + -
694B PRO 5.5 5.8 - - - -
695B ILE* 4.3 19.3 - - + +
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Residues in contact with ALA 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A LEU* 5.9 2.8 - - + +
676A GLN* 4.2 25.1 - - + +
677A GLU 3.6 2.5 + - - +
678A PRO 3.2 1.0 + - - -
679A TRP* 1.3 76.7 - - - +
681A PHE* 1.3 76.1 + - + +
682A ARG 3.8 0.5 + - - -
688A GLU* 5.2 3.6 - - - +
691A ARG* 5.0 6.2 + - - -
695B ILE* 4.7 20.8 - - - +
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Residues in contact with PHE 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A GLN 4.1 18.6 - - - -
677A GLU 4.6 1.3 - - - -
678A PRO 2.9 8.6 + - - +
680A ALA* 1.3 89.8 - - + +
682A ARG* 1.3 66.3 + - - +
683A GLY 3.3 0.2 + - - -
684A GLY* 3.0 18.9 + - - +
688A GLU* 4.1 18.3 - - - +
691A ARG* 4.9 1.6 - - - +
290B ARG* 3.5 27.4 + - - +
568B PRO 3.7 13.7 - - - -
569B TYR* 3.3 43.3 - + + -
570B GLU* 3.9 4.3 - - - -
571B HIS* 4.2 20.4 - + - -
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Residues in contact with ARG 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LYS* 3.9 7.3 - - - +
645A TRP* 4.0 3.4 - - - -
646A ASP* 3.0 27.9 + - - -
649A SER* 3.9 17.6 + - - -
650A ILE* 3.2 20.4 - - - +
678A PRO* 3.5 5.9 + - - +
679A TRP* 3.3 60.5 + - + +
680A ALA 3.5 1.6 + - - -
681A PHE* 1.3 77.5 - - - +
683A GLY* 1.3 61.2 + - - +
684A GLY 3.4 2.1 + - - +
687A GLY* 4.4 0.2 - - - -
691A ARG* 2.9 29.3 + - - +
286B TYR 3.1 26.0 + - - -
287B ASP* 3.3 23.2 + - - +
690B GLN* 3.5 30.8 + - - +
695B ILE* 5.4 3.8 - - + +
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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