Contacts of the helix formed by residues 651 - 657 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624F LYS* 6.1 1.3 - - + +
642F LEU* 3.7 20.0 - - + -
647F LEU* 3.7 23.1 - - + -
649F ARG 4.1 0.7 - - - +
650F ILE* 1.3 97.4 - - + +
652F HIS* 1.3 65.1 + - - +
653F ALA* 4.4 8.7 - - + +
654F ILE* 3.6 28.8 - - + +
679F PHE* 4.1 4.7 - - - -
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Residues in contact with HIS 652 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650F ILE 3.5 2.4 + - - -
651F PRO* 1.3 72.7 - - + +
653F ALA* 1.3 67.5 + - + +
654F ILE* 3.2 8.7 + - - +
655F PHE* 3.2 29.3 + + - +
674F GLU* 4.8 14.1 + - + +
678F SER* 5.2 12.0 + - - +
679F PHE* 5.3 6.6 - - - -
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Residues in contact with ALA 653 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628F LEU* 3.7 31.8 - - + +
631F LEU* 3.3 30.9 - - + +
651F PRO* 3.4 5.7 - - + +
652F HIS* 1.3 89.1 + - + +
654F ILE* 1.3 61.6 + - - +
655F PHE* 3.2 12.1 + - - -
656F SER* 4.0 2.1 + - - -
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Residues in contact with ILE 654 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631F LEU* 4.9 8.3 - - + -
640F LEU* 4.0 22.9 - - + -
642F LEU* 6.2 2.5 - - + -
650F ILE* 5.5 3.6 - - + -
651F PRO* 3.6 26.1 + - + +
652F HIS 3.2 0.9 - - - +
653F ALA* 1.3 76.1 - - - +
655F PHE* 1.3 64.7 + - - +
656F SER 3.2 2.6 + - - -
657F LEU* 3.5 38.1 - - + +
660F LEU* 4.0 20.4 - - + +
679F PHE* 4.2 9.9 - - + -
682F LEU* 3.9 22.0 - - + +
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Residues in contact with PHE 655 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652F HIS* 3.2 26.9 - + - +
653F ALA* 3.2 9.3 - - - -
654F ILE* 1.3 79.0 - - + +
656F SER* 1.3 72.2 + - - +
657F LEU 3.4 7.4 + - - +
678F SER* 4.0 19.3 - - - +
679F PHE* 5.7 1.1 - - + -
681F HIS* 4.5 26.1 - + + +
682F LEU* 3.6 34.9 - - + +
684F ARG* 5.4 1.4 + - - -
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Residues in contact with SER 656 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631F LEU* 3.7 31.6 + - - +
632F LYS* 4.5 9.0 + - - +
635F MET* 4.0 12.6 - - - +
653F ALA 4.5 1.3 - - - -
654F ILE 3.2 2.4 - - - -
655F PHE* 1.3 92.1 - - - +
657F LEU* 1.3 64.5 + - - +
658F SER* 3.7 2.3 + - - -
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Residues in contact with LEU 657 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631F LEU* 4.1 18.6 + - + +
634F MET* 3.2 20.9 - - - +
635F MET* 3.8 7.9 - - - +
637F VAL* 3.4 31.9 - - + +
640F LEU* 4.8 3.1 - - + -
654F ILE* 3.5 39.4 + - + +
655F PHE 3.6 9.0 - - - +
656F SER* 1.3 80.1 - - - +
658F SER* 1.3 66.8 + - - +
659F ASN 3.3 26.0 - - - +
660F LEU* 3.7 22.9 - - + +
682F LEU* 4.3 1.9 - - - +
684F ARG* 5.0 0.7 - - - -
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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