Contacts of the helix formed by residues 625 - 636 (chain A) in PDB entry 2QR8
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 625 (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 4.3 6.5 - - - +
624A ASP* 1.3 74.7 - - - +
626A PRO* 1.3 75.3 - - + +
627A GLU* 3.5 11.9 + - - +
628A GLU* 2.8 38.5 + - - +
629A ILE* 3.2 20.5 + - - +
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Residues in contact with PRO 626 (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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624A ASP 3.8 2.6 - - - +
625A THR* 1.3 89.3 - - + +
627A GLU* 1.3 72.8 + - - +
629A ILE* 3.4 5.1 + - + +
630A LEU* 2.9 39.3 + - + +
705A ALA 5.5 0.7 - - - +
708A SER* 6.2 0.9 - - - +
709A ALA* 3.9 26.9 - - + +
712A ARG* 6.4 1.6 - - + -
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Residues in contact with GLU 627 (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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625A THR* 3.5 12.3 + - - +
626A PRO* 1.3 96.9 - - - +
628A GLU* 1.3 60.4 + - - +
630A LEU* 3.4 8.0 + - - +
631A ALA* 2.8 29.2 + - - +
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Residues in contact with GLU 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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623A ASP 4.5 0.5 - - - +
624A ASP* 3.2 14.7 - - - +
625A THR* 2.8 46.5 + - - +
627A GLU* 1.3 76.0 - - - +
629A ILE* 1.3 64.8 + - - +
631A ALA* 3.4 7.7 + - - +
632A ARG* 3.2 56.9 + - - +
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Residues in contact with ILE 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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618A PHE* 3.6 25.8 - - + +
619A ALA* 3.7 12.8 - - + -
624A ASP* 3.9 15.5 - - + +
625A THR 3.2 16.2 + - - +
626A PRO* 3.7 6.5 - - + +
628A GLU* 1.3 75.5 - - - +
630A LEU* 1.3 62.7 + - - +
632A ARG* 3.2 6.2 + - - +
633A ILE* 3.0 38.9 + - + +
705A ALA* 3.6 42.2 - - + +
706A THR* 4.0 18.8 - - + +
709A ALA* 4.0 10.3 - - + -
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Residues in contact with LEU 630 (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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626A PRO* 2.9 26.2 + - + +
627A GLU* 3.4 6.5 + - - +
629A ILE* 1.3 75.9 - - - +
631A ALA* 1.3 56.2 + - - +
633A ILE* 3.4 13.3 + - + +
634A GLY* 2.9 26.3 + - - -
709A ALA* 3.9 17.9 - - + +
710A LEU* 4.1 23.6 - - + -
712A ARG* 3.1 35.4 - - - +
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Residues in contact with ALA 631 (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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627A GLU 2.8 18.3 + - - +
628A GLU* 3.6 10.1 - - - +
629A ILE 3.2 0.2 - - - -
630A LEU* 1.3 76.5 - - - +
632A ARG* 1.3 62.4 + - + +
634A GLY* 3.2 1.7 + - - -
635A SER* 3.0 21.5 + - - -
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Residues in contact with ARG 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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617A PRO 5.1 2.0 - - - +
618A PHE* 2.9 49.1 + - + +
619A ALA* 3.7 2.6 - - - +
620A ASN* 3.9 16.4 - - - +
624A ASP* 2.7 30.1 + - - -
628A GLU* 3.2 44.2 + - - +
629A ILE* 3.6 6.2 - - - +
631A ALA* 1.3 76.1 - - + +
633A ILE* 1.3 63.7 + - - +
635A SER* 3.0 26.8 + - - +
636A GLY 3.7 1.6 + - - -
637A LYS 4.3 2.5 - - - +
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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
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602A TRP* 4.0 28.5 - - + +
618A PHE* 3.6 30.8 - - + -
629A ILE* 3.0 33.3 + - + +
630A LEU* 3.7 15.7 - - + +
632A ARG* 1.3 75.4 - - - +
634A GLY* 1.3 62.9 + - - +
636A GLY* 3.3 9.9 + - - -
662A VAL* 3.8 12.1 - - + +
706A THR* 4.6 1.6 - - + -
710A LEU* 3.8 33.7 - - + -
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Residues in contact with GLY 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 LEU 2.9 15.0 + - - -
631A ALA* 3.7 3.6 - - - -
633A ILE* 1.3 76.8 - - - +
635A SER* 1.3 60.0 + - - +
636A GLY 3.2 0.9 + - - -
662A VAL* 4.1 13.8 - - - +
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Residues in contact with SER 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 ALA 3.0 12.6 + - - -
632A ARG* 3.0 18.9 + - - -
634A GLY* 1.3 75.3 - - - +
636A GLY* 1.3 59.7 + - - +
637A LYS* 3.0 37.7 + - - +
662A VAL* 5.5 0.7 - - - +
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Residues in contact with GLY 636 (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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618A PHE* 6.2 0.7 - - - -
632A ARG 3.7 1.0 + - - -
633A ILE 3.3 8.3 + - - -
634A GLY 3.2 4.8 - - - -
635A SER* 1.3 77.6 + - - +
637A LYS* 1.3 62.7 + - - +
638A PHE* 4.2 16.7 - - - -
660A LEU 5.5 0.7 - - - -
662A VAL* 3.7 31.8 + - - +
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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