Contacts of the helix formed by residues 620 - 630 (chain C) in PDB entry 2HYE
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 620 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537C THR* 6.0 2.1 - - - +
539C MET* 3.9 31.8 - - + +
540C GLU* 4.2 10.9 - - - +
614C LYS* 5.1 1.1 - - - +
619C ILE* 1.3 88.6 - - - +
621C ASP* 1.3 60.7 + - - +
622C SER* 4.0 15.2 + - - +
623C GLU* 2.7 7.1 + - + +
624C LEU* 2.7 35.3 + - - -
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Residues in contact with ASP 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C PHE* 3.1 13.8 - - - -
614C LYS* 3.2 27.8 + - - +
620C GLU* 1.3 71.4 - - - +
622C SER* 1.3 66.0 + - - +
623C GLU 3.1 0.9 + - - -
624C LEU* 4.5 4.3 - - - -
625C ARG* 2.5 74.3 + - - +
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Residues in contact with SER 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C GLU* 4.0 17.8 + - - +
621C ASP* 1.3 79.0 + - - +
623C GLU* 1.3 60.4 + - - +
625C ARG* 4.1 6.0 - - - +
626C ARG* 3.4 24.7 + - - +
679C GLU* 4.6 20.6 - - - -
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Residues in contact with GLU 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C MET* 5.1 6.0 - - - +
572C THR* 5.3 6.4 - - - +
594C PHE* 3.5 34.1 - - + -
619C ILE* 4.3 7.6 - - + -
620C GLU* 2.7 16.0 + - + +
622C SER* 1.3 75.3 + - - +
624C LEU* 1.3 55.0 + - - +
625C ARG 2.6 17.5 + - - -
626C ARG* 2.7 51.4 + - - +
627C THR* 2.8 25.7 + - - +
672C ILE* 5.2 6.2 - - - +
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Residues in contact with LEU 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C VAL* 4.7 7.2 - - + -
610C PHE* 4.0 19.7 - - + -
613C ILE* 3.9 15.9 - - + -
614C LYS* 3.8 37.2 - - + +
619C ILE* 3.6 29.2 - - + +
620C GLU 2.7 20.7 + - - +
621C ASP* 4.3 2.0 - - - +
623C GLU* 1.3 72.1 - - - +
625C ARG* 1.3 57.1 + - - +
627C THR* 3.8 8.5 - - - -
628C LEU* 2.8 50.9 + - + +
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Residues in contact with ARG 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C PHE* 3.0 29.0 - - - -
614C LYS* 5.1 0.2 - - - +
621C ASP* 2.5 56.4 + - - +
622C SER* 4.1 7.2 - - - +
623C GLU 2.6 4.6 + - - +
624C LEU* 1.3 73.6 - - - +
626C ARG* 1.3 52.1 + - + +
628C LEU* 2.9 9.1 + - - +
629C GLN* 2.4 37.5 + - + +
648C VAL* 3.7 39.5 + - + +
649C GLU* 3.7 13.2 + - - -
650C ASP* 4.3 13.7 + - - -
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Residues in contact with ARG 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622C SER* 3.4 21.7 + - - +
623C GLU* 2.7 51.0 + - - +
625C ARG* 1.3 70.5 - - + +
627C THR* 1.3 54.7 + - - +
628C LEU 2.8 5.6 - - - -
629C GLN* 2.7 39.7 + - + +
630C SER 3.0 9.9 + - - -
672C ILE* 3.3 28.9 + - + +
677C THR* 3.8 32.3 - - - +
679C GLU* 4.0 15.6 + - - -
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Residues in contact with THR 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C SER* 4.7 0.7 - - - +
594C PHE* 3.5 42.2 - - + +
595C GLN* 3.8 12.8 - - + +
598C VAL* 4.9 5.9 - - + +
619C ILE* 4.8 1.7 - - + +
623C GLU* 2.8 41.8 + - - +
624C LEU* 3.7 11.0 + - + -
626C ARG* 1.3 76.1 - - - +
628C LEU* 1.3 57.5 + - - +
630C SER* 3.1 1.4 + - - -
631C LEU* 2.9 29.3 - - - +
672C ILE* 4.0 12.7 - - + +
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Residues in contact with LEU 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C VAL* 4.0 28.5 - - + -
610C PHE* 3.9 19.7 - - + -
613C ILE* 4.4 10.5 - - + -
624C LEU* 2.8 42.0 + - + +
625C ARG* 3.1 5.4 - - - +
627C THR* 1.3 77.6 - - - +
629C GLN* 1.3 54.3 + - - +
630C SER 2.3 24.9 - - - +
631C LEU* 4.3 8.3 - - + +
632C ALA* 4.0 10.9 + - - +
633C CYS* 5.0 0.3 - - - -
639C LEU* 5.8 2.0 - - + -
648C VAL* 4.5 5.3 - - + +
654C PHE* 3.5 47.6 - - + -
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Residues in contact with GLN 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C ARG* 2.4 18.6 + - - +
626C ARG* 2.7 33.2 + - + +
628C LEU* 1.3 73.4 - - - +
630C SER* 1.3 59.5 + - - +
633C CYS* 3.0 32.1 + - + +
634C GLY* 3.3 7.3 + - - -
646C LYS 3.9 17.2 + - - +
647C GLU* 3.6 21.8 + - - +
648C VAL* 4.3 15.7 - - + +
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Residues in contact with SER 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595C GLN* 2.8 5.5 + - - -
626C ARG 3.0 3.6 + - - -
627C THR 3.1 1.0 + - - -
628C LEU 2.3 30.1 - - - +
629C GLN* 1.3 74.0 - - - +
631C LEU* 1.3 84.0 + - - +
632C ALA 2.6 17.4 + - - +
634C GLY* 4.9 6.7 - - - +
669C ILE* 4.3 7.2 - - - -
672C ILE* 2.8 37.2 - - - +
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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