Contacts of the helix formed by residues 623 - 634 (chain A) in PDB entry 4G3D
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 ALA 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A GLU* 2.9 21.6 + - - +
621A SER 3.8 1.0 + - - -
622A CYS* 1.3 70.4 - - - +
624A PRO* 1.3 76.7 - - + +
625A LEU* 4.3 1.6 - - + +
626A THR* 2.8 20.7 + - - +
627A ALA* 3.0 9.9 + - - +
654A ALA 5.2 1.1 - - - +
657A GLN* 4.2 17.5 - - + +
658A VAL* 3.8 19.7 - - + -
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Residues in contact with PRO 624 (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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622A CYS 3.5 5.8 - - - +
623A ALA* 1.3 84.5 - - + +
625A LEU* 1.3 57.5 + - - +
627A ALA* 3.4 8.3 + - + +
628A GLN* 2.8 31.1 + - - +
657A GLN* 4.4 12.8 - - - +
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Residues in contact with LEU 625 (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 ALA* 3.0 1.6 + - + -
624A PRO* 1.3 76.9 - - - +
626A THR* 1.3 60.6 + - - +
628A GLN* 3.6 18.8 - - + +
629A ALA* 2.9 26.7 + - - +
650A LYS* 3.7 34.8 - - + +
653A ARG* 4.5 22.0 - - + +
654A ALA* 4.1 11.8 - - + +
657A GLN* 3.2 25.7 + - + +
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Residues in contact with THR 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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489A GLU* 2.7 28.0 + - + +
493A LEU* 3.7 30.8 - - + +
586A MET* 4.1 9.6 - - + -
590A LEU* 4.6 0.7 - - + -
622A CYS* 4.4 12.3 - - - -
623A ALA* 2.8 15.6 + - - +
625A LEU* 1.3 74.9 - - - +
627A ALA* 1.3 65.6 + - - +
629A ALA* 3.2 5.9 + - - +
630A ILE* 3.0 41.3 + - + +
654A ALA* 3.8 9.5 + - - +
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Residues in contact with ALA 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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618A ILE* 3.9 30.4 - - + +
622A CYS* 4.7 6.0 - - + +
623A ALA 3.0 7.1 + - - +
624A PRO* 3.6 11.2 - - + +
626A THR* 1.3 80.3 - - - +
628A GLN* 1.3 56.8 + - - +
630A ILE* 3.5 2.7 + - - +
631A GLN* 2.8 44.3 + - - +
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Residues in contact with GLN 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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624A PRO 2.8 19.0 + - - +
625A LEU* 3.6 22.2 - - + +
626A THR 3.2 0.2 - - - -
627A ALA* 1.3 73.7 - - - +
629A ALA* 1.3 59.7 + - - +
631A GLN* 3.1 14.7 + - + +
632A GLU* 2.8 52.1 + - - +
650A LYS* 4.1 10.8 + - + +
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Residues in contact with ALA 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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493A LEU* 5.9 1.1 - - + -
496A LEU* 6.1 0.9 - - + -
583A CYS* 4.9 0.2 - - - -
625A LEU* 2.9 18.6 + - - +
626A THR* 3.2 8.2 + - - +
628A GLN* 1.3 75.7 - - - +
630A ILE* 1.3 63.7 + - + +
632A GLU* 3.3 1.3 + - - -
633A GLY* 2.9 19.6 + - - -
647A LEU* 3.3 29.9 - - + +
650A LYS* 4.1 22.8 - - + +
651A VAL* 4.4 15.3 - - + +
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Residues in contact with ILE 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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496A LEU* 5.7 2.0 - - + -
583A CYS* 4.0 13.5 - - + -
586A MET* 3.8 33.0 - - + -
587A LEU* 4.5 11.0 - - + -
590A LEU* 4.0 12.3 - - + -
618A ILE* 3.7 32.5 - - + -
626A THR* 3.0 31.9 + - + +
627A ALA* 3.7 3.8 - - - +
629A ALA* 1.3 77.0 - - + +
631A GLN* 1.3 65.6 + - - +
633A GLY 3.1 1.7 + - - -
634A LEU* 2.9 45.6 + - + +
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Residues in contact with GLN 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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615A VAL* 3.5 37.8 - - + +
618A ILE* 3.9 6.7 - - + -
627A ALA* 2.8 37.5 + - - +
628A GLN* 3.1 12.7 + - + +
630A ILE* 1.3 73.1 - - - +
632A GLU* 1.3 63.3 + - - +
634A LEU* 3.1 20.1 + - - +
635A ARG* 3.7 5.6 + - - +
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Residues in contact with GLU 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 GLN* 2.8 33.4 + - - +
629A ALA* 3.9 3.4 - - - +
631A GLN* 1.3 73.0 - - - +
633A GLY* 1.3 62.2 + - - +
635A ARG* 3.2 51.1 + - - +
641A ARG* 3.6 8.7 - - - +
642A VAL* 3.7 28.5 + - + -
650A LYS* 2.5 40.1 + - + +
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Residues in contact with GLY 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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579A VAL* 3.7 16.4 - - - +
580A TRP* 3.6 17.0 - - - -
583A CYS* 3.7 17.7 - - - -
629A ALA 2.9 11.8 + - - -
630A ILE 3.1 4.5 + - - -
632A GLU* 1.3 76.2 - - - +
634A LEU* 1.3 59.9 + - - +
635A ARG 3.5 0.9 - - - -
641A ARG* 3.4 19.8 - - - -
642A VAL* 4.4 4.8 - - - +
647A LEU* 4.6 0.7 - - - -
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Residues in contact with LEU 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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580A TRP* 3.5 52.9 - - + +
583A CYS* 3.7 12.6 - - + -
584A CYS* 4.3 5.8 - - - -
587A LEU* 4.1 17.9 - - + -
613A PRO* 3.2 32.6 - - + +
614A PRO* 4.0 18.6 - - + -
615A VAL* 4.3 11.6 - - + +
630A ILE* 2.9 34.6 + - + +
631A GLN* 3.1 9.2 + - - +
632A GLU 3.1 0.6 - - - -
633A GLY* 1.3 78.3 - - - +
635A ARG* 1.3 61.0 + - - +
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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