Contacts of the helix formed by residues 627 - 640 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623B ASP 4.5 5.7 + - - -
624B LEU* 2.9 42.0 - - + +
625B LEU 3.3 4.4 + - - -
626B ARG* 1.3 77.4 + - - +
628B PRO* 1.4 72.0 - - - +
629B LEU* 3.4 17.0 - - + +
630B PHE* 3.2 22.1 + - + +
631B ASP* 3.2 27.8 + - - +
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Residues in contact with PRO 628 (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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594B VAL* 5.5 1.8 - - + -
626B ARG 4.6 0.9 - - - +
627B THR* 1.4 88.1 - - - +
629B LEU* 1.3 65.3 + - - +
631B ASP* 3.2 12.5 + - + +
632B GLN* 2.9 43.8 + - - +
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Residues in contact with LEU 629 (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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588B VAL* 4.1 11.4 - - + -
592B ALA* 3.5 26.7 - - + +
594B VAL* 3.7 40.9 - - + +
597B VAL* 3.9 22.8 - - + +
598B THR* 4.9 0.5 + - - -
620B ILE* 6.5 0.2 - - + -
624B LEU* 4.4 19.5 - - + -
627B THR* 3.3 12.3 - - + +
628B PRO* 1.3 78.3 - - - +
630B PHE* 1.3 65.3 + - + +
632B GLN* 3.5 5.0 + - - +
633B ILE* 3.3 43.4 + - + +
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Residues in contact with PHE 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B ILE* 3.4 49.4 - - + -
624B LEU* 3.0 23.8 - - + +
625B LEU* 3.4 23.8 - - + +
627B THR* 3.2 9.1 - - + +
629B LEU* 1.3 79.4 - - + +
631B ASP* 1.3 72.6 + - - +
633B ILE* 3.2 15.7 + - + +
634B ILE* 3.1 41.4 + - + +
650B PHE* 3.5 37.9 - + - -
654B LEU* 6.3 0.9 - - + -
675B ILE* 4.7 2.5 - - + -
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Residues in contact with ASP 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B LEU 5.1 1.9 - - - +
626B ARG 5.6 0.5 - - - -
627B THR 3.2 18.9 + - - +
628B PRO* 3.2 11.1 + - + +
630B PHE* 1.3 82.3 - - - +
632B GLN* 1.3 55.4 + - + +
634B ILE* 3.1 17.7 - - + +
635B ASP* 2.8 45.3 + - - +
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Residues in contact with GLN 632 (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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594B VAL* 3.5 34.3 - - - +
598B THR* 3.9 16.2 + - + +
628B PRO* 2.9 35.2 + - - +
629B LEU* 3.6 5.3 - - - +
631B ASP* 1.3 76.8 - - + +
633B ILE* 1.3 56.1 + - - +
635B ASP* 3.6 10.0 - - - +
636B MSE 3.0 30.8 + - - +
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Residues in contact with ILE 633 (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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588B VAL* 4.8 6.3 - - + -
597B VAL* 3.3 34.3 - - + -
598B THR* 4.3 11.9 - - - +
601B VAL* 4.7 2.9 - - + -
618B LEU* 4.1 25.8 - - + -
620B ILE* 5.1 4.5 - - + -
629B LEU* 3.3 24.4 + - + +
630B PHE* 3.2 21.4 + - + +
632B GLN* 1.3 76.1 - - - +
634B ILE* 1.3 60.5 + - + +
636B MSE 3.3 14.9 + - + +
637B LEU* 2.9 50.4 + - + +
675B ILE* 5.0 2.2 - - + -
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Residues in contact with ILE 634 (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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630B PHE* 3.1 39.7 + - + +
631B ASP* 3.1 32.5 - - + +
633B ILE* 1.3 72.6 - - + +
635B ASP* 1.4 91.2 + - - +
637B LEU* 3.0 9.9 + - - +
638B ARG* 3.0 40.7 + - - +
644B ILE* 4.7 18.2 - - + +
650B PHE* 5.6 2.5 - - + -
675B ILE* 4.9 7.6 - - + -
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Residues in contact with ASP 635 (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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631B ASP* 2.8 34.1 + - - +
632B GLN* 3.6 10.6 - - - +
634B ILE* 1.4 78.1 - - - +
636B MSE 1.3 62.5 + - - +
638B ARG* 3.0 33.7 + - - +
639B VAL* 3.1 27.2 + - + +
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Residues in contact with MSE 636 (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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598B THR* 3.5 31.2 - - + +
601B VAL* 3.6 23.1 - - + -
602B ARG* 3.5 46.7 - - - +
606B CYS* 4.7 1.3 - - - -
632B GLN 3.0 19.7 + - - +
633B ILE* 3.3 13.2 - - + +
635B ASP* 1.3 74.7 - - - +
637B LEU* 1.3 70.1 + - + +
639B VAL* 3.1 12.3 + - + +
640B GLU* 2.7 58.2 + - + +
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Residues in contact with LEU 637 (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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601B VAL* 4.3 5.6 - - + -
605B LYS* 5.1 4.5 - - + -
606B CYS* 5.4 0.7 - - - -
633B ILE* 2.9 35.6 + - + +
634B ILE* 3.0 7.6 + - - +
636B MSE 1.3 97.9 - - + +
638B ARG* 1.4 58.0 + - - +
640B GLU* 3.3 2.7 + - - +
641B GLN 3.0 9.0 + - - -
642B VAL* 3.0 52.7 + - + +
644B ILE* 3.9 19.1 - - + -
673B LEU* 3.9 24.2 - - + -
675B ILE* 3.9 23.6 - - + -
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Residues in contact with ARG 638 (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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634B ILE* 3.0 26.8 + - - +
635B ASP* 3.0 45.9 + - - +
637B LEU* 1.4 71.7 - - - +
639B VAL* 1.4 81.2 + - + +
641B GLN* 3.0 21.6 + - - +
642B VAL 5.1 2.0 - - - +
644B ILE* 5.9 0.6 - - - +
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Residues in contact with VAL 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B ASP* 3.1 16.1 + - + +
636B MSE 3.2 10.8 - - - +
638B ARG* 1.4 84.1 - - + +
640B GLU* 1.3 67.7 + - + +
641B GLN* 3.3 10.7 + - - +
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Residues in contact with GLU 640 (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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602B ARG* 3.5 26.8 + - + -
606B CYS* 3.7 27.0 - - - +
636B MSE 2.7 42.6 + - + +
637B LEU 3.8 3.8 - - - +
638B ARG 3.2 0.4 - - - -
639B VAL* 1.3 79.8 - - + +
641B GLN* 1.3 69.2 + - - +
642B VAL* 3.4 6.8 + - + +
671B LEU* 3.6 15.9 - - - +
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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