Contacts of the helix formed by residues 626 - 638 (chain A) in PDB entry 2VGE
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 626 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624A ARG 4.6 6.0 + - - +
625A LEU* 1.3 73.4 - - - +
627A PRO* 1.3 70.7 - - + +
628A LEU* 3.3 2.7 - - + +
629A VAL* 3.1 34.8 + - + +
630A LEU* 3.3 13.4 + - - +
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Residues in contact with PRO 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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621A ARG* 3.7 42.0 - - - +
625A LEU 3.2 10.0 - - - +
626A ASN* 1.3 83.7 - - + +
628A LEU* 1.3 59.2 + - - +
630A LEU* 3.2 7.8 + - + +
631A LEU* 2.9 26.9 + - - +
646A ALA* 5.6 2.1 - - - +
649A GLU* 5.2 6.1 - - - +
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Residues in contact with LEU 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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626A ASN* 3.3 2.8 + - + +
627A PRO* 1.3 80.4 - - - +
629A VAL* 1.3 60.4 + - + +
631A LEU* 3.1 24.8 + - + +
632A LEU* 2.9 42.7 + - + +
650A MET* 4.7 1.8 - - + -
655A GLN* 3.7 37.2 - - + +
656A PRO 3.6 23.1 - - - +
657A ASN* 3.7 19.1 - - + -
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Residues in contact with VAL 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A ASN* 3.1 32.9 + - + +
628A LEU* 1.3 80.3 - - + +
630A LEU* 1.3 67.7 + - + +
632A LEU* 3.4 8.9 + - + +
633A ASP* 2.8 41.5 + - - +
657A ASN* 6.6 0.2 - - + -
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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
----------------------------------------------------------
621A ARG* 3.6 41.7 - - + -
625A LEU* 4.1 30.3 - - + -
626A ASN 3.6 11.0 - - - +
627A PRO* 3.2 7.8 + - + +
629A VAL* 1.3 79.2 - - + +
631A LEU* 1.3 59.8 + - - +
633A ASP* 3.5 10.7 + - + +
634A ALA* 3.0 30.5 + - - +
642A VAL* 4.6 8.7 - - + +
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Residues in contact with LEU 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 PRO 2.9 13.6 + - - +
628A LEU* 3.3 22.7 - - + +
630A LEU* 1.3 76.2 - - - +
632A LEU* 1.3 58.9 + - + +
634A ALA* 3.2 5.5 + - - +
635A ALA* 2.9 25.3 + - - +
642A VAL* 5.3 2.5 - - - -
643A VAL* 4.1 26.0 - - + +
646A ALA* 3.6 26.7 - - + -
647A VAL* 5.3 2.2 - - + -
650A MET* 3.7 37.2 - - + -
653A PRO 5.4 0.7 - - - +
655A GLN 5.5 0.7 - - - +
663A ALA* 4.0 27.8 - - + +
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Residues in contact with LEU 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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628A LEU* 2.9 33.7 + - + +
629A VAL* 3.9 7.6 - - - +
630A LEU 3.4 0.2 - - - -
631A LEU* 1.3 76.2 - - + +
633A ASP* 1.3 59.8 + - - +
635A ALA* 3.3 3.8 + - - +
636A LEU* 2.9 22.2 + - - +
657A ASN* 3.5 35.2 - - + +
661A ILE* 3.9 16.6 - - + +
662A THR* 3.5 9.4 - - - +
663A ALA* 3.3 36.3 - - + +
666A ASN* 3.0 25.9 + - - +
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Residues in contact with ASP 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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629A VAL* 2.8 35.1 + - - +
630A LEU* 3.8 11.2 - - + +
632A LEU* 1.3 77.4 - - - +
634A ALA* 1.3 58.1 + - - +
636A LEU* 3.0 12.1 + - - +
637A THR* 2.8 40.9 + - + +
666A ASN* 5.5 0.7 + - - -
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Residues in contact with ALA 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 3.0 18.6 + - - +
631A LEU 3.6 4.9 - - - +
633A ASP* 1.3 76.0 - - - +
635A ALA* 1.3 57.3 + - - +
637A THR* 3.8 7.6 - - - -
638A GLY* 2.9 23.6 + - - -
639A GLU* 2.9 24.0 + - + +
642A VAL* 3.6 32.8 - - + -
643A VAL* 4.2 7.2 - - + +
675A ILE* 5.0 0.3 - - - +
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Residues in contact with ALA 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 LEU 2.9 16.1 + - - +
632A LEU 3.6 5.2 - - - +
634A ALA* 1.3 77.4 - - - +
636A LEU* 1.3 57.2 + - - +
638A GLY* 4.6 0.3 - - - -
643A VAL* 4.1 14.1 - - + +
663A ALA* 3.4 36.3 - - + +
666A ASN* 4.1 2.2 - - + -
667A ALA* 3.2 21.1 - - + +
672A ASN* 3.0 22.2 + - - +
675A ILE* 4.5 5.6 - - + +
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Residues in contact with LEU 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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632A LEU 2.9 17.8 + - - +
633A ASP* 3.5 12.8 - - - +
635A ALA* 1.3 78.9 - - - +
637A THR* 1.3 63.2 + - + +
666A ASN* 3.7 37.0 - - + +
669A CYS* 4.4 10.8 - - + -
670A GLY* 3.6 19.6 - - - +
672A ASN* 3.2 11.8 + - - -
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Residues in contact with THR 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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633A ASP* 2.8 28.0 + - + +
634A ALA* 3.7 8.5 + - - -
636A LEU* 1.3 81.1 - - + +
638A GLY* 1.3 61.0 + - - +
639A GLU* 4.0 12.9 - - - +
672A ASN* 3.8 6.3 - - - +
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Residues in contact with GLY 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 ALA 2.9 7.9 + - - -
636A LEU 3.6 1.8 - - - -
637A THR* 1.3 80.7 - - - +
639A GLU* 1.3 65.6 + - - +
640A LEU* 3.2 8.4 + - - +
672A ASN* 3.4 24.1 - - - +
675A ILE* 3.8 12.7 - - - +
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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