Contacts of the helix formed by residues 623 - 634 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489E GLU* 2.7 20.0 + - - +
622E CYS* 1.3 74.7 - - - +
624E PRO* 1.4 75.0 - - + +
625E LEU 3.3 0.7 - - - +
626E THR* 3.0 21.2 + - - +
627E ALA* 3.1 9.9 + - - +
654E ALA* 5.7 0.9 - - + +
657E GLN* 4.2 20.0 - - - +
658E VAL* 4.2 16.6 - - + -
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Residues in contact with PRO 624 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D GLU* 3.3 53.6 - - + +
505D TYR* 5.6 0.4 - - - -
508D SER* 4.2 18.4 - - - +
645D ALA* 4.3 6.1 - - + -
622E CYS 4.2 3.4 - - - +
623E ALA* 1.4 85.1 - - + +
625E LEU* 1.3 55.4 + - - +
627E ALA* 3.3 8.6 + - + +
628E GLN* 3.0 31.4 + - - +
657E GLN* 4.4 1.6 - - - +
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Residues in contact with LEU 625 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645D ALA* 3.8 35.0 - - + +
646D GLU* 4.6 15.7 - - + +
649D GLY* 5.2 7.2 - - - -
623E ALA* 3.3 0.8 - - + -
624E PRO* 1.3 76.3 - - - +
626E THR* 1.3 64.7 + - - +
628E GLN* 4.2 4.4 - - + +
629E ALA* 3.2 25.3 + - + +
650E LYS* 3.4 31.9 - - + +
653E ARG* 4.1 20.2 - - + +
654E ALA* 3.8 19.9 - - + +
657E GLN* 3.2 26.2 + - + +
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Residues in contact with THR 626 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489E GLU* 3.1 27.0 + - + +
493E LEU* 3.8 34.3 - - + +
586E MET* 4.4 7.9 - - + -
590E LEU* 4.9 1.3 - - + -
622E CYS* 4.7 7.9 - - - -
623E ALA* 3.0 15.6 + - - +
625E LEU* 1.3 77.0 - - - +
627E ALA* 1.3 63.7 + - - +
629E ALA* 3.4 4.9 + - - +
630E ILE* 3.0 44.7 + - + +
654E ALA* 3.8 11.0 + - - +
658E VAL* 5.2 0.2 - - - +
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Residues in contact with ALA 627 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618E ILE* 3.6 26.5 - - + +
619E PRO 5.9 0.2 - - - +
622E CYS* 4.6 9.1 - - + +
623E ALA 3.1 11.7 + - - +
624E PRO* 3.3 11.4 + - + +
626E THR* 1.3 76.3 - - - +
628E GLN* 1.3 51.5 + - - +
630E ILE* 3.1 5.6 + - - +
631E GLN* 2.7 44.7 + - - +
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Residues in contact with GLN 628 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D LYS* 5.9 2.7 - - - +
643D SER* 3.0 35.0 + - - -
645D ALA* 5.4 2.4 - - - +
646D GLU* 4.0 20.5 - - - +
624E PRO 3.0 16.5 + - - +
625E LEU* 4.2 5.1 - - + +
627E ALA* 1.3 75.4 - - - +
629E ALA* 1.3 55.5 + - - +
631E GLN* 3.0 16.5 + - + +
632E GLU* 2.8 62.9 + - + +
650E LYS* 5.9 0.4 - - + -
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Residues in contact with ALA 629 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493E LEU* 6.2 0.7 - - + -
583E CYS* 4.4 0.2 - - - -
625E LEU 3.2 19.3 + - - +
626E THR* 3.4 7.4 - - - +
627E ALA 3.3 0.2 - - - -
628E GLN* 1.3 78.2 - - - +
630E ILE* 1.3 64.0 + - + +
632E GLU* 4.0 4.0 - - - +
633E GLY* 3.1 17.5 + - - -
647E LEU* 3.4 33.3 - - + +
650E LYS* 4.4 23.3 - - + -
651E VAL* 4.7 9.6 - - + -
654E ALA* 5.5 0.4 - - + -
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Residues in contact with ILE 630 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496E LEU* 5.7 2.2 - - + -
583E CYS* 4.0 18.3 - - + +
586E MET* 3.8 30.3 - - + -
587E LEU* 4.1 15.7 - - + -
590E LEU* 4.4 10.8 - - + -
615E VAL* 6.3 1.1 - - + -
618E ILE* 3.8 25.1 - - + -
622E CYS* 5.2 0.7 - - - -
626E THR* 3.0 31.8 + - + +
627E ALA* 3.5 5.6 - - - +
629E ALA* 1.3 75.3 - - + +
631E GLN* 1.3 61.6 + - - +
633E GLY* 3.1 3.3 + - - -
634E LEU* 3.0 46.1 + - + +
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Residues in contact with GLN 631 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615E VAL* 3.4 41.1 - - + +
618E ILE* 4.5 10.0 - - + +
627E ALA* 2.7 22.4 + - - +
628E GLN* 3.5 22.1 - - + +
630E ILE* 1.3 74.4 - - - +
632E GLU* 1.3 62.4 + - + +
634E LEU* 3.3 19.9 + - - +
635E ARG* 3.6 5.5 - - - +
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Residues in contact with GLU 632 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628E GLN* 2.8 47.3 + - + +
629E ALA* 4.2 2.9 - - - +
631E GLN* 1.3 73.8 - - + +
633E GLY* 1.3 60.1 - - - +
634E LEU 3.2 0.7 - - - -
635E ARG* 3.2 46.8 + - - +
641E ARG* 3.8 1.7 - - - +
642E VAL* 3.7 30.4 + - + -
650E LYS* 2.7 36.0 + - + +
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Residues in contact with GLY 633 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579E VAL* 3.9 8.1 - - - +
580E TRP* 3.6 17.0 + - - -
583E CYS* 3.9 13.0 - - - -
629E ALA 3.1 15.1 + - - -
630E ILE 3.1 5.8 + - - -
632E GLU* 1.3 77.1 - - - +
634E LEU* 1.3 60.6 + - - +
635E ARG 3.6 0.9 - - - -
641E ARG* 3.5 20.7 - - - -
642E VAL* 4.1 11.8 - - - +
647E LEU* 4.6 0.7 - - - -
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Residues in contact with LEU 634 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580E TRP* 3.6 54.7 - - + +
583E CYS* 3.9 10.3 - - + -
584E CYS* 4.0 10.1 - - - -
587E LEU* 4.1 20.2 - - + -
613E PRO* 3.5 23.5 - - + +
614E PRO* 4.4 20.4 - - + -
615E VAL* 4.3 13.6 - - + +
630E ILE* 3.0 32.1 + - + +
631E GLN 3.3 10.6 + - - +
632E GLU 3.2 0.8 - - - -
633E GLY* 1.3 78.2 - - - +
635E ARG* 1.3 59.3 + - - +
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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