Contacts of the helix formed by residues 649 - 661 (chain D) in PDB entry 5LS6
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 ASP 649 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D ASP* 4.5 4.8 - - - +
647D SER* 3.2 9.1 + - - +
648D GLN* 1.3 77.9 - - - +
650D GLU* 1.3 66.0 + - - +
652D ASP* 3.0 18.1 + - - +
653D ARG* 3.2 37.2 + - - +
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Residues in contact with GLU 650 (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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123D GLU 4.5 1.3 - - - +
124D ASP* 3.4 20.3 - - - +
125D GLU* 2.7 42.6 + - - +
153D TYR* 4.7 1.0 + - - -
646D ILE* 4.0 25.4 - - + -
647D SER* 3.2 4.9 + - - +
649D ASP* 1.3 79.0 - - - +
651D ALA* 1.3 56.8 + - - +
653D ARG* 2.3 43.8 + - - +
654D ARG* 3.0 62.8 + - - +
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Residues in contact with ALA 651 (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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646D ILE* 4.1 10.6 - - + +
647D SER 3.3 17.7 + - - +
648D GLN* 4.6 6.7 - - - +
650D GLU* 1.3 79.3 - - - +
652D ASP* 1.3 52.5 + - - +
654D ARG* 3.7 0.8 - - - +
655D GLY* 2.7 32.4 + - - -
666D LEU* 3.8 16.4 - - + +
674D VAL* 3.8 31.9 - - + -
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Residues in contact with ASP 652 (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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152D ASN* 4.2 10.7 - - - +
648D GLN* 3.0 23.0 + - - +
649D ASP* 3.0 12.3 + - - +
651D ALA* 1.3 75.9 - - - +
653D ARG* 1.3 63.6 + - + +
655D GLY* 4.0 1.7 - - - +
656D LYS* 3.3 27.5 + - - +
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Residues in contact with ARG 653 (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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124D ASP* 4.0 15.6 + - - +
125D GLU* 2.9 18.0 + - - +
126D THR* 5.3 6.4 - - - +
149D LEU* 4.8 3.5 - - - +
152D ASN* 3.5 39.5 + - + +
153D TYR* 3.6 43.8 + - + +
649D ASP* 3.3 36.4 + - - +
650D GLU* 2.3 50.2 + - - +
652D ASP* 1.3 76.9 - - + +
654D ARG* 1.3 64.8 + - + +
655D GLY 3.5 0.3 + - - -
656D LYS* 3.5 11.6 + - - +
657D VAL* 3.6 11.6 + - - +
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Residues in contact with ARG 654 (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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122D VAL* 4.4 11.7 - - - +
123D GLU 5.0 0.8 + - - -
125D GLU* 5.4 1.3 - - - +
153D TYR* 5.1 5.2 - - - +
644D GLU* 2.8 25.9 + - - -
646D ILE* 3.9 32.2 - - - +
650D GLU* 3.0 40.7 + - - +
651D ALA* 4.1 3.8 - - - +
653D ARG* 1.3 74.4 - - - +
655D GLY* 1.3 60.8 + - - +
657D VAL* 3.3 8.5 - - + +
658D TYR* 2.9 57.2 + - + +
666D LEU* 4.7 1.6 - - + -
676D ASP* 2.7 37.8 + - - +
679D ARG* 2.9 40.4 - - - +
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Residues in contact with GLY 655 (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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651D ALA 2.7 24.0 + - - -
652D ASP* 4.0 3.4 - - - -
653D ARG 3.2 0.4 - - - -
654D ARG* 1.3 75.7 - - - +
656D LYS* 1.3 51.5 + - - +
658D TYR* 3.7 1.2 - - - +
659D ASP* 2.7 45.1 + - - +
664D SER* 5.3 0.7 - - - -
666D LEU* 3.5 18.6 - - - -
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Residues in contact with LYS 656 (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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145D PHE* 4.0 21.4 - - - -
148D GLU* 3.6 43.6 + - - +
149D LEU* 4.0 11.9 - - + +
152D ASN* 3.2 36.8 - - - +
652D ASP 3.3 10.8 + - - +
653D ARG* 3.8 9.2 - - - +
654D ARG 3.2 0.6 - - - -
655D GLY* 1.3 76.5 - - - +
657D VAL* 1.3 62.8 + - - +
659D ASP* 3.3 10.7 + - - +
660D LYS* 3.2 20.6 + - - +
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Residues in contact with VAL 657 (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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132D PRO* 3.4 33.9 - - + -
134D MET* 5.9 0.2 - - - -
145D PHE* 4.5 5.4 - - + -
149D LEU* 4.2 19.2 - - + +
153D TYR* 6.2 0.2 - - - +
653D ARG 3.6 3.6 + - - +
654D ARG* 3.3 19.7 + - + +
656D LYS* 1.3 80.2 - - - +
658D TYR* 1.3 75.4 + - + +
660D LYS* 3.1 19.9 + - + +
661D TYR* 3.2 23.5 - - + -
809D 74D 4.1 17.0 - - + -
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Residues in contact with TYR 658 (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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654D ARG* 2.9 41.2 + - + +
655D GLY 4.1 1.6 - - - +
657D VAL* 1.3 85.6 - - + +
659D ASP* 1.3 63.3 + - - +
660D LYS 3.2 1.8 - - - -
661D TYR* 3.5 5.8 + - - +
662D MET 3.4 10.9 + - - -
663D CYS 3.2 22.5 + - - +
664D SER* 3.5 26.4 + - - -
665D PHE 4.4 0.7 - - - -
666D LEU* 3.9 19.3 - - + -
676D ASP* 3.1 28.2 + - - -
678D THR* 3.1 36.2 - - + +
679D ARG* 4.4 10.9 + - - -
809D 74D 3.5 36.4 - - + +
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Residues in contact with ASP 659 (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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655D GLY* 2.7 31.8 + - - +
656D LYS* 3.3 11.3 + - - +
658D TYR* 1.3 72.3 - - - +
660D LYS* 1.3 64.3 + - + +
662D MET* 3.4 22.7 + - - +
663D CYS 5.5 0.2 - - - +
664D SER* 5.1 7.7 + - - -
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Residues in contact with LYS 660 (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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134D MET* 4.1 19.8 - - + +
142D ASP 5.5 4.1 - - - +
145D PHE* 3.3 67.5 - - + -
656D LYS 3.2 5.3 + - - +
657D VAL* 3.1 14.6 + - + +
659D ASP* 1.3 77.1 - - - +
661D TYR* 1.3 56.2 + - - +
662D MET* 3.1 31.3 + - + +
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Residues in contact with TYR 661 (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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111D TYR* 4.1 13.2 - - - -
132D PRO* 3.3 23.0 - - + +
133D TYR 4.5 5.1 + - - -
134D MET* 4.3 24.6 - - + +
657D VAL* 3.2 33.8 + - + -
658D TYR 3.5 2.1 + - - +
659D ASP 3.5 0.4 - - - -
660D LYS* 1.3 75.7 - - - +
662D MET* 1.3 64.7 + - - +
663D CYS* 2.9 11.3 + - - +
809D 74D 3.4 94.9 - + + -
237E ASP* 5.1 1.7 + - - -
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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