Contacts of the helix formed by residues 623 - 634 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489D GLU* 2.7 22.2 + - - +
622D CYS* 1.3 75.6 - - - +
624D PRO* 1.3 74.5 - - + +
625D LEU* 3.3 0.7 - - + -
626D THR* 3.2 14.6 + - - +
627D ALA* 3.1 19.4 + - - +
654D ALA 5.4 4.3 - - - +
657D GLN* 3.6 23.3 - - + +
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Residues in contact with PRO 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622D CYS 3.8 2.7 - - - +
623D ALA* 1.3 83.5 - - - +
625D LEU* 1.3 55.3 + - - +
627D ALA* 3.4 6.8 + - + +
628D GLN* 3.1 28.7 + - - +
657D GLN* 3.5 20.6 - - - +
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Residues in contact with LEU 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623D ALA 3.3 0.8 - - - -
624D PRO* 1.3 77.5 - - - +
626D THR* 1.3 65.4 + - - +
628D GLN* 3.9 17.6 - - - +
629D ALA* 3.1 21.9 + - + +
650D LYS* 3.4 37.5 - - + +
653D ARG* 3.8 30.3 - - + +
654D ALA* 4.1 7.9 - - + -
657D GLN* 3.5 24.4 + - + +
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Residues in contact with THR 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D GLU* 3.0 26.6 + - + +
493D LEU* 3.9 23.2 - - + +
586D MET* 4.4 9.4 - - + -
590D LEU* 4.8 0.2 - - + -
622D CYS* 4.0 15.9 - - + -
623D ALA* 3.2 18.7 + - - +
625D LEU* 1.3 79.4 - - - +
627D ALA* 1.3 63.0 + - - +
629D ALA* 3.5 4.2 + - - +
630D ILE* 3.3 38.1 + - + +
654D ALA* 3.7 18.4 + - - +
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Residues in contact with ALA 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D ILE* 3.4 33.8 - - + +
619D PRO 5.6 0.4 - - - +
622D CYS* 5.1 5.8 - - + -
623D ALA 3.1 9.1 + - - +
624D PRO* 3.8 9.2 - - + +
626D THR* 1.3 77.0 - - - +
628D GLN* 1.3 61.0 + - - +
630D ILE* 3.1 3.6 + - - -
631D GLN* 2.9 35.3 + - - +
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Residues in contact with GLN 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624D PRO 3.1 18.6 + - - +
625D LEU* 3.9 17.0 - - - +
626D THR 3.4 0.2 - - - -
627D ALA* 1.3 75.7 - - - +
629D ALA* 1.3 56.6 + - - +
631D GLN* 3.3 18.3 + - - +
632D GLU* 3.0 58.2 + - + +
650D LYS* 4.2 10.7 + - - +
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Residues in contact with ALA 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D LEU* 6.3 1.1 - - + -
625D LEU* 3.1 19.0 + - + +
626D THR* 3.6 7.2 - - - +
628D GLN* 1.3 76.9 - - - +
630D ILE* 1.3 56.5 + - + +
632D GLU* 3.4 9.0 + - - +
633D GLY* 3.0 23.4 + - - -
647D LEU* 3.2 28.9 - - + +
650D LYS* 4.4 23.3 - - + +
651D VAL* 4.9 9.0 - - + -
654D ALA* 6.0 0.4 - - + -
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Residues in contact with ILE 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D LEU* 5.8 2.0 - - + -
583D CYS* 4.0 16.1 - - + +
586D MET* 3.8 30.7 - - + -
587D LEU* 4.3 16.2 - - + -
590D LEU* 4.5 9.6 - - + -
615D VAL* 5.9 0.2 - - - -
618D ILE* 3.7 30.1 - - + -
619D PRO* 5.6 0.4 - - + -
622D CYS* 5.8 0.2 - - - -
626D THR* 3.3 28.9 + - + +
627D ALA 3.1 7.0 + - - +
629D ALA* 1.3 73.4 - - + +
631D GLN* 1.3 60.7 + - - +
633D GLY* 3.1 2.4 + - - -
634D LEU* 2.9 50.0 + - + +
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Residues in contact with GLN 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D VAL* 3.4 43.5 - - + +
618D ILE* 4.2 5.8 - - + -
627D ALA* 2.9 18.3 + - - +
628D GLN* 3.5 25.4 - - - +
630D ILE* 1.3 76.0 - - - +
632D GLU* 1.3 58.7 + - + +
633D GLY 3.1 0.2 - - - -
634D LEU* 3.1 16.5 + - - +
635D ARG* 3.4 14.6 + - - +
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Residues in contact with GLU 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628D GLN* 3.0 44.6 + - + +
629D ALA* 3.9 3.5 - - - +
631D GLN* 1.3 76.7 - - + +
633D GLY* 1.3 57.1 + - - +
635D ARG* 3.4 33.8 + - - +
641D ARG* 3.7 1.0 - - - +
642D VAL* 3.4 36.2 + - + -
647D LEU* 5.8 0.2 - - + -
650D LYS* 2.7 37.5 + - + +
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Residues in contact with GLY 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579D VAL* 4.3 4.5 - - - -
580D TRP* 3.7 14.2 + - - -
583D CYS* 3.7 18.2 - - - -
629D ALA 3.0 10.9 + - - -
630D ILE 3.1 5.3 + - - -
632D GLU* 1.3 79.1 - - - +
634D LEU* 1.3 58.1 + - - +
635D ARG 3.4 2.7 - - - -
641D ARG* 3.3 26.4 + - - -
642D VAL* 4.2 8.5 - - - +
647D LEU* 4.7 0.7 - - - -
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Residues in contact with LEU 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580D TRP* 3.3 48.2 - - + +
583D CYS* 3.7 22.2 - - + -
584D CYS* 4.3 10.3 - - - +
587D LEU* 3.9 20.2 - - + -
613D PRO* 3.3 23.3 - - + +
614D PRO* 4.0 23.6 - - + +
615D VAL* 4.2 8.4 - - + +
630D ILE* 2.9 34.1 + - + +
631D GLN 3.1 7.1 + - - +
633D GLY* 1.3 76.1 - - - +
635D ARG* 1.3 62.2 + - - +
636D LYS 3.4 0.9 + - - -
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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