Contacts of the helix formed by residues 673 - 683 (chain B) in PDB entry 1MZC
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 ASN 673 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634B GLN* 2.9 26.5 + - + +
635B SER 5.8 1.1 - - - +
636B PRO* 5.3 2.2 + - - +
638B GLY* 5.3 1.0 - - - -
671B ILE 3.3 2.5 + - - +
672B ILE* 1.3 72.0 - - - +
674B ARG* 1.3 56.3 + - - +
675B GLU* 3.3 15.6 - - - +
676B LYS* 3.0 42.6 + - + +
677B LEU* 2.9 27.7 + - - +
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Residues in contact with ARG 674 (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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672B ILE* 3.1 23.3 + - + +
673B ASN* 1.3 70.5 + - - +
675B GLU* 1.3 79.4 + - - +
677B LEU* 3.7 7.3 - - - +
678B LEU* 3.1 18.9 + - - +
714B THR* 2.8 24.8 + - - -
715B ASN* 2.9 31.9 + - - +
716B ILE* 3.8 11.5 - - + +
915B PHE* 3.7 25.3 - - + -
918B LYS* 3.8 31.9 + - - +
919B PRO* 3.0 27.7 + - - +
921B PRO* 3.6 18.4 - - + +
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Residues in contact with GLU 675 (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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673B ASN* 3.3 13.1 - - - +
674B ARG* 1.3 92.5 + - - +
676B LYS* 1.3 65.2 + - + +
678B LEU* 3.5 3.3 + - - +
679B GLN* 3.3 34.5 + - - +
921B PRO* 3.7 24.2 - - + +
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Residues in contact with LYS 676 (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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635B SER 5.2 0.4 - - - +
636B PRO 3.2 24.0 + - - +
637B GLU* 3.4 17.1 - - - +
638B GLY* 3.5 17.7 - - - +
673B ASN* 3.0 34.0 + - + +
675B GLU* 1.3 76.8 - - + +
677B LEU* 1.3 60.8 + - - +
679B GLN* 3.1 32.7 + - - +
680B TYR* 2.8 30.3 + - - +
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Residues in contact with LEU 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B GLN* 5.8 0.7 - - - +
638B GLY* 4.0 0.4 - - - -
639B GLY* 4.0 20.9 - - - +
640B PHE* 5.7 2.2 - - + -
653B THR* 3.9 24.9 - - + -
657B VAL* 4.8 5.6 - - + -
672B ILE* 3.9 23.8 - - + -
673B ASN 2.9 19.0 + - - +
674B ARG* 3.7 6.7 - - - +
676B LYS* 1.3 77.4 - - - +
678B LEU* 1.3 62.1 + - - +
680B TYR* 3.2 7.4 + - + +
681B LEU* 3.0 32.9 + - + +
710B VAL* 4.5 18.4 - - + -
714B THR* 4.0 14.1 - - + +
716B ILE* 3.7 20.6 - - + -
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Residues in contact with LEU 678 (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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674B ARG 3.1 16.3 + - - +
675B GLU 3.9 4.3 - - - +
676B LYS 3.3 0.2 - - - -
677B LEU* 1.3 76.2 - - - +
679B GLN* 1.3 63.4 + - + +
681B LEU* 3.3 3.3 + - + +
682B TYR* 3.0 53.0 + - + -
716B ILE* 3.2 41.0 - - + +
718B THR* 4.0 16.2 - - + -
721B LEU* 4.1 14.1 - - + -
920B VAL* 4.0 6.5 - - + -
921B PRO* 3.9 29.6 - - + +
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Residues in contact with GLN 679 (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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637B GLU 5.0 1.1 - - - +
675B GLU* 3.3 20.9 + - - +
676B LYS* 3.1 43.4 + - - +
678B LEU* 1.3 78.5 - - + +
680B TYR* 1.3 58.3 + - - +
682B TYR* 3.2 10.2 + - - +
683B SER* 2.9 28.2 + - - -
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Residues in contact with TYR 680 (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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637B GLU* 3.7 25.2 + - - +
638B GLY 3.6 18.8 - - - -
639B GLY* 4.0 8.1 - - - -
648B PRO* 3.0 47.9 + - + -
649B HIS* 3.3 7.2 + - - -
650B LEU* 4.6 8.7 - - + -
653B THR* 4.3 12.1 - - - -
676B LYS 2.8 17.1 + - - +
677B LEU* 3.4 8.1 - - + +
679B GLN* 1.3 74.2 - - - +
681B LEU* 1.3 74.3 + - + +
683B SER* 2.5 33.8 + - - -
684B LEU* 3.3 39.3 + - + +
694B HIS* 3.8 8.0 - - - -
695B VAL* 4.5 5.4 - - + -
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Residues in contact with LEU 681 (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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650B LEU* 3.6 31.6 - - + -
677B LEU* 3.0 20.2 + - + +
678B LEU* 3.6 7.0 - - - +
680B TYR* 1.3 81.7 - - + +
682B TYR* 1.3 64.9 + - - +
684B LEU* 3.0 16.4 + - + +
685B LYS 3.2 9.5 + - - -
691B PHE* 3.7 11.9 - - + -
707B ALA* 4.0 21.3 - - + +
710B VAL* 4.3 8.7 - - + -
711B ALA* 3.9 27.8 - - + -
716B ILE* 4.0 16.4 - - + -
721B LEU* 4.1 21.3 - - + -
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Residues in contact with TYR 682 (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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678B LEU* 3.0 46.8 + - + +
679B GLN* 3.3 13.0 - - - +
681B LEU* 1.3 74.7 - - - +
683B SER* 1.3 59.0 + - - +
684B LEU 3.0 5.2 + - - -
685B LYS* 3.2 22.8 + - + +
718B THR* 2.8 32.7 + - + +
720B ASP* 2.9 28.3 + - - -
721B LEU* 3.9 15.9 - - + -
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Residues in contact with SER 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLU* 5.0 2.3 + - - -
679B GLN 2.9 13.1 + - - -
680B TYR* 2.5 35.3 + - - -
682B TYR* 1.3 75.1 - - - +
684B LEU* 1.3 65.7 + - - +
685B LYS 5.3 0.7 - - - -
686B GLN* 5.4 0.9 + - - -
692B LEU* 4.9 5.4 - - - +
695B VAL* 4.5 10.6 - - - +
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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