Contacts of the helix formed by residues 621 - 627 (chain G) in PDB entry 4MNE
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 ALA 621 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619G TRP 3.7 1.4 + - - -
620G MET* 1.3 73.0 - - - +
622G PRO* 1.3 65.7 - - + +
623G GLU* 3.2 22.2 - - - +
624G VAL* 2.8 36.4 + - + +
625G ILE* 3.1 9.0 + - - +
637G SER* 4.4 6.4 + - - +
640G TYR* 3.4 35.7 - - + -
704G ARG* 3.8 2.0 - - - +
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Residues in contact with PRO 622 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620G MET 4.4 0.9 - - - +
621G ALA* 1.3 86.6 - - + +
623G GLU* 1.3 62.3 + - - +
625G ILE* 3.4 6.0 + - + +
626G ARG* 3.1 51.7 + - - +
640G TYR* 3.9 17.3 - - + +
669G VAL* 3.7 36.1 - - + +
670G GLY* 4.1 1.5 - - - +
672G GLY* 5.6 1.1 - - - +
674G LEU 6.1 0.2 - - - +
699G LYS* 4.1 25.1 - - + +
704G ARG* 3.8 8.1 - - - +
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Residues in contact with GLU 623 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621G ALA* 3.7 9.1 - - - +
622G PRO* 1.3 70.9 - - - +
624G VAL* 1.3 64.8 + - + +
626G ARG* 3.4 24.2 + - - +
627G MET* 3.2 16.8 + - - -
628G GLN 4.6 1.2 + - - -
629G ASP* 4.6 13.4 - - - +
632G PRO* 3.5 30.6 - - + +
637G SER* 4.4 5.4 + - - -
699G LYS 3.7 7.7 - - - +
701G ARG* 3.3 27.7 - - + +
704G ARG* 2.5 46.1 + - - -
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Residues in contact with VAL 624 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613G LEU* 3.6 5.3 - - + +
620G MET* 3.5 21.8 - - + -
621G ALA* 2.8 26.9 + - + +
623G GLU* 1.3 70.5 - - + +
625G ILE* 1.3 66.2 - - - +
627G MET* 3.3 23.2 - - - +
632G PRO* 4.0 14.6 - - - +
633G TYR* 3.3 44.9 - - + +
637G SER* 3.7 29.8 - - - -
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Residues in contact with ILE 625 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613G LEU* 4.1 7.4 - - + +
617G ILE* 4.8 7.6 - - + +
620G MET* 3.6 33.9 - - + +
621G ALA 3.6 9.2 - - - +
622G PRO* 3.5 7.6 - - + +
624G VAL* 1.3 79.7 - - - +
626G ARG* 1.3 61.4 + - - +
627G MET* 4.1 5.2 - - - +
665G ILE* 4.7 1.3 - - + +
666G ILE* 3.5 48.0 - - + +
669G VAL* 3.6 37.7 - - + -
670G GLY* 4.0 3.8 - - - +
309H ALA* 5.3 0.3 - - - +
310H ILE* 5.5 0.5 - - - +
311H PHE* 3.2 23.1 + - + +
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Residues in contact with ARG 626 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622G PRO* 3.1 42.3 + - - +
623G GLU* 3.4 29.2 + - - +
624G VAL 3.3 0.2 - - - -
625G ILE* 1.3 74.6 - - - +
627G MET* 1.3 69.3 + - - +
628G GLN* 3.2 35.9 + - + +
629G ASP* 4.3 11.4 + - - +
670G GLY* 2.8 26.1 + - - +
671G ARG* 6.3 0.2 - - - +
672G GLY* 5.9 0.8 - - - +
699G LYS* 4.3 10.9 + - - +
309H ALA* 4.4 4.7 - - - +
311H PHE* 3.8 33.4 - - + +
312H GLU* 5.0 2.3 + - - +
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Residues in contact with MET 627 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611G GLU 4.0 20.4 - - - +
613G LEU* 3.9 39.5 - - + +
623G GLU 3.2 11.8 + - - -
624G VAL 3.3 18.8 - - - +
625G ILE 4.1 1.6 - - - +
626G ARG* 1.3 78.1 - - - +
628G GLN* 1.3 59.5 + - - +
629G ASP 3.9 4.4 - - - +
632G PRO* 3.8 26.5 - - + -
633G TYR* 4.9 7.2 - - + -
309H ALA* 3.8 21.1 - - + +
312H GLU* 5.4 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