Contacts of the helix formed by residues 651 - 657 (chain D) in PDB entry 6M04
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 PRO 651 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624D LYS 5.7 0.7 - - - +
625D LEU* 6.3 1.1 - - - -
626D LEU* 6.0 6.1 - - + +
642D LEU* 3.7 29.8 - - + -
647D LEU* 3.7 30.7 - - + -
649D ARG 4.0 2.0 - - - +
650D ILE* 1.3 91.7 - - + +
652D HIS* 1.3 63.8 + - - +
653D ALA* 3.2 6.1 + - + +
654D ILE* 3.6 26.4 - - + +
663D LEU* 5.7 4.5 - - + -
665D LEU* 4.8 8.5 - - + -
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Residues in contact with HIS 652 (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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650D ILE 3.1 4.6 + - - -
651D PRO* 1.3 72.9 - - - +
653D ALA* 1.3 64.7 + - + +
654D ILE* 3.2 5.0 + - - +
655D PHE* 3.1 28.4 + + - +
674D GLU* 3.3 34.5 + - + +
675D GLU* 6.0 2.5 - - + -
678D SER* 5.1 5.5 + - - -
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Residues in contact with ALA 653 (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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626D LEU 5.6 1.8 - - - +
628D LEU* 4.2 28.7 - - + +
631D LEU* 3.4 29.3 - - + +
651D PRO* 3.2 4.2 - - + +
652D HIS* 1.3 86.9 - - + +
654D ILE* 1.3 56.9 + - - +
655D PHE* 3.1 20.4 + - + -
656D SER* 3.7 6.6 + - - -
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Residues in contact with ILE 654 (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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626D LEU* 6.3 1.1 - - + -
631D LEU* 4.6 11.0 - - + -
634D MET* 4.0 9.0 - - + -
640D LEU* 3.8 24.5 - - + -
642D LEU* 5.9 2.5 - - + -
650D ILE* 5.2 4.3 - - + -
651D PRO* 3.6 23.6 + - + +
652D HIS* 3.2 2.0 - - - -
653D ALA* 1.3 73.6 - - - +
655D PHE* 1.3 64.2 + - - +
656D SER 3.1 3.6 + - - -
657D LEU* 3.8 27.9 + - + +
660D LEU* 3.7 24.4 - - + +
663D LEU* 4.2 14.4 - - + -
679D PHE* 5.3 3.6 - - + -
682D LEU* 3.6 27.6 - - + +
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Residues in contact with PHE 655 (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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628D LEU* 6.0 2.7 - - + -
652D HIS* 3.1 30.7 + + - +
653D ALA* 3.1 16.6 - - + -
654D ILE* 1.3 75.3 - - - +
656D SER* 1.3 65.5 + - - +
657D LEU 3.0 17.0 + - - +
658D SER* 5.3 1.6 + - - -
678D SER* 4.0 28.0 - - - +
681D HIS* 5.3 13.2 - - + +
682D LEU* 3.8 18.7 - - + +
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Residues in contact with SER 656 (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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628D LEU* 4.9 7.0 - - - +
631D LEU* 3.8 26.8 - - - +
632D LYS* 4.6 11.6 + - - +
635D MET* 3.8 17.3 - - - +
653D ALA 3.9 3.8 - - - -
654D ILE 3.1 2.0 - - - -
655D PHE* 1.3 89.0 - - - +
657D LEU* 1.3 58.8 + - - +
658D SER* 5.7 0.2 - - - -
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Residues in contact with LEU 657 (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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631D LEU* 3.9 11.9 - - + +
634D MET* 3.3 45.3 - - + +
635D MET* 3.7 15.0 - - + -
637D VAL* 3.8 5.4 - - + -
654D ILE* 3.8 33.7 - - + +
655D PHE 3.0 3.5 + - - +
656D SER* 1.3 79.3 - - - +
658D SER* 1.3 60.4 + - - +
659D ASN* 3.3 37.8 + - - +
660D LEU* 3.7 13.9 - - + -
682D LEU* 3.3 21.8 - - - +
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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