Contacts of the helix formed by residues 627 - 640 (chain A) in PDB entry 2H5G
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 THR 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623A ASP 4.9 3.1 - - - -
624A LEU* 2.8 45.8 + - + +
625A LEU 3.4 1.8 + - - -
626A ARG* 1.3 77.4 - - - +
628A PRO* 1.4 76.2 - - - +
629A LEU* 3.5 15.4 + - + +
630A PHE* 3.1 22.7 + - + +
631A ASP* 3.2 22.3 + - - +
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Residues in contact with PRO 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A VAL* 5.7 1.3 - - + -
626A ARG 4.6 1.3 - - - +
627A THR* 1.4 89.9 - - - +
629A LEU* 1.3 64.1 + - - +
631A ASP* 3.2 11.8 + - + +
632A GLN* 2.9 42.8 + - - +
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Residues in contact with LEU 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A VAL* 4.2 8.7 - - + -
592A ALA* 3.5 26.9 - - + +
594A VAL* 3.6 40.4 - - + +
597A VAL* 3.8 25.7 - - + +
598A THR* 5.0 0.7 + - - -
620A ILE* 6.2 0.7 - - + -
624A LEU* 4.1 25.1 - - + -
627A THR* 3.2 12.2 - - + +
628A PRO* 1.3 79.6 - - - +
630A PHE* 1.3 64.1 + - - +
632A GLN* 3.4 6.2 + - - +
633A ILE* 3.3 33.9 + - + +
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Residues in contact with PHE 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A ILE* 3.7 38.6 - - + -
624A LEU* 3.1 26.2 - - + +
625A LEU* 3.8 31.0 - - + +
627A THR* 3.1 11.5 - - + +
629A LEU* 1.3 78.4 - - - +
631A ASP* 1.3 77.1 + - - +
633A ILE* 3.2 11.1 + - + +
634A ILE* 3.2 46.4 + - + +
650A PHE* 4.2 26.7 - + - -
675A ILE* 4.9 2.9 - - + -
677A VAL* 6.3 0.2 - - + -
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Residues in contact with ASP 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU 5.4 0.9 - - - +
627A THR 3.2 11.4 + - - +
628A PRO* 3.2 15.1 + - + +
630A PHE* 1.3 89.2 - - - +
632A GLN* 1.3 57.9 + - + +
634A ILE* 3.1 19.2 - - + +
635A ASP* 2.9 29.6 + - - +
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Residues in contact with GLN 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A VAL* 3.8 29.9 - - - +
598A THR* 3.8 19.0 + - + +
628A PRO* 2.9 42.6 + - - +
629A LEU* 3.8 5.3 - - - +
630A PHE 3.3 0.2 - - - -
631A ASP* 1.3 77.5 - - + +
633A ILE* 1.3 56.4 + - - +
635A ASP* 3.6 9.0 - - + +
636A MSE 2.9 29.1 + - - +
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Residues in contact with ILE 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A VAL* 4.6 12.6 - - + -
597A VAL* 3.5 32.8 - - + -
598A THR* 4.5 8.3 - - - +
601A VAL* 4.7 5.2 - - + -
618A LEU* 4.0 17.3 - - + -
620A ILE* 4.6 16.2 - - + -
629A LEU* 3.3 24.7 + - + +
630A PHE* 3.2 13.6 + - + +
631A ASP 3.1 0.8 - - - -
632A GLN* 1.3 71.9 - - - +
634A ILE* 1.3 70.5 + - + +
636A MSE 3.0 13.9 + - + +
637A LEU* 2.8 42.0 + - + +
675A ILE* 5.4 0.9 - - + -
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Residues in contact with ILE 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A PHE* 3.2 38.9 + - + +
631A ASP* 3.1 35.2 - - + +
633A ILE* 1.3 79.0 - - + +
635A ASP* 1.4 61.7 + - + +
637A LEU* 3.4 16.4 + - + +
638A ARG* 2.8 35.8 + - + +
644A ILE* 5.6 7.0 - - + -
650A PHE* 6.2 0.7 - - + -
675A ILE* 5.3 6.1 - - + -
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Residues in contact with ASP 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A ASP 2.9 18.2 + - - +
632A GLN* 3.6 10.3 - - + +
634A ILE* 1.4 80.8 - - + +
636A MSE 1.3 57.5 + - - +
638A ARG* 3.1 7.0 + - - +
639A VAL* 2.9 30.8 + - - +
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Residues in contact with MSE 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A THR* 3.4 37.0 - - + +
601A VAL* 3.6 22.4 - - + -
602A ARG* 3.3 70.4 - - + +
606A CYS* 4.7 2.0 - - - -
632A GLN 2.9 10.0 + - - +
633A ILE* 3.7 7.4 - - + +
635A ASP* 1.3 74.6 - - - +
637A LEU* 1.3 76.4 + - + +
639A VAL* 3.1 9.6 + - + +
640A GLU* 2.9 32.6 + - - +
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A VAL* 4.4 4.5 - - + -
605A LYS* 5.2 4.9 - - + -
606A CYS* 5.7 0.2 - - - -
633A ILE* 2.8 33.1 + - + +
634A ILE* 3.5 13.2 - - - +
636A MSE 1.3 93.6 - - + +
638A ARG* 1.4 57.1 + - - +
640A GLU* 3.5 2.4 + - - -
641A GLN 3.2 5.4 + - - -
642A VAL* 2.8 51.8 + - + +
644A ILE* 3.8 15.0 - - + -
673A LEU* 3.8 23.6 - - + -
675A ILE* 3.7 30.7 - - + -
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Residues in contact with ARG 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ILE 2.8 19.9 + - - +
635A ASP* 3.1 4.9 + - - +
637A LEU* 1.4 71.9 - - - +
639A VAL* 1.4 63.2 + - - +
640A GLU 3.1 0.2 - - - -
641A GLN* 3.0 26.1 + - - +
642A VAL 5.3 1.6 - - - -
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Residues in contact with VAL 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A ARG* 6.2 0.9 - - - +
635A ASP* 2.9 15.8 + - + +
636A MSE 3.1 11.0 + - + +
638A ARG* 1.4 79.6 - - - +
640A GLU* 1.3 72.3 + - - +
641A GLN* 3.1 13.2 + - - +
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Residues in contact with GLU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A ARG* 4.0 24.8 + - + +
606A CYS* 3.0 43.5 - - + +
636A MSE 2.9 18.5 + - - +
637A LEU 4.1 3.8 - - - +
638A ARG 3.1 0.4 - - - -
639A VAL* 1.3 89.5 - - - +
641A GLN* 1.4 67.7 + - - +
642A VAL* 3.3 10.7 + - + +
671A LEU* 4.1 12.4 - - + +
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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