Contacts of the helix formed by residues 646 - 653 (chain D) in PDB entry 5X22
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 LYS 646 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B GLN* 4.1 16.6 - - - +
644D LEU 4.3 1.1 - - - -
645D PRO* 1.3 72.0 - - - +
647D ARG* 1.3 66.4 + - + +
649D ALA* 3.2 1.2 + - - +
650D LEU* 2.9 31.9 + - - +
688D TRP* 3.6 52.7 - - + +
691D LEU* 4.0 1.9 - - + +
692D GLU* 5.8 2.2 - - - +
720D LEU* 4.3 26.7 - - + -
721D VAL 3.1 19.8 + - - +
722D GLU* 3.1 39.4 + - - +
723D GLY 4.5 1.4 + - - +
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Residues in contact with ARG 647 (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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1005C MET* 4.1 25.7 - - + +
1007C ALA* 5.4 0.2 - - - +
645D PRO* 3.2 2.4 - - + +
646D LYS* 1.3 85.8 - - + +
648D MET* 1.3 61.9 + - - +
650D LEU* 3.5 24.5 - - - +
651D GLU* 3.8 6.6 + - - +
680D GLN* 3.4 42.5 - - - +
683D ILE* 4.5 10.7 - - - +
688D TRP* 3.8 33.4 - - - +
723D GLY 5.5 5.2 - - - +
724D GLN* 5.6 6.1 - - + -
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Residues in contact with MET 648 (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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1005C MET* 3.6 39.7 - - + -
1006C HIS 4.0 13.2 - - - +
1007C ALA* 3.8 15.2 - - + +
627D GLY 4.3 1.1 - - - -
628D ARG 4.1 10.1 - - - +
629D SER* 3.8 16.4 - - - -
644D LEU* 4.2 8.1 - - + -
645D PRO* 3.3 25.1 + - + +
646D LYS 3.2 0.6 - - - -
647D ARG* 1.3 75.3 - - - +
649D ALA* 1.3 61.6 + - - +
650D LEU 3.1 2.0 - - - -
651D GLU* 3.0 6.6 + - - +
652D LEU* 2.9 43.3 + - + +
726D ILE* 4.5 1.1 - - - -
747D VAL* 3.7 30.1 - - + -
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Residues in contact with ALA 649 (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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644D LEU* 3.7 14.6 - - + +
645D PRO 3.1 8.6 + - - +
646D LYS 3.2 2.9 + - - +
648D MET* 1.3 79.1 - - - +
650D LEU* 1.3 56.1 + - - +
652D LEU* 3.8 7.6 - - - +
653D PHE* 2.9 48.2 + - + +
691D LEU* 3.9 9.0 - - + +
695D ILE* 5.1 0.4 - - + -
720D LEU* 3.6 29.8 - - + -
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Residues in contact with LEU 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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646D LYS 2.9 16.6 + - - +
647D ARG* 3.5 18.8 - - - +
649D ALA* 1.3 76.6 - - - +
651D GLU* 1.3 65.0 + - + +
653D PHE 4.0 0.3 - - - -
654D LYS* 3.2 33.2 + - - +
657D LEU* 3.6 29.2 - - + +
677D LEU* 3.9 24.0 - - + +
683D ILE* 4.4 19.7 - - + -
687D VAL* 5.0 3.4 - - + -
688D TRP* 4.3 23.1 - - + -
691D LEU* 3.9 10.2 - - - +
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Residues in contact with GLU 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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1007C ALA* 3.3 30.3 - - + +
1008C ARG* 3.7 1.1 - - - -
1009C SER* 3.0 56.2 + - - +
1010C THR 4.4 0.7 - - - +
1027C PHE* 3.6 21.8 - - + -
647D ARG 3.8 6.0 + - - +
648D MET 3.0 7.2 + - - +
650D LEU* 1.3 81.3 - - + +
652D LEU* 1.3 67.1 + - - +
654D LYS* 3.2 36.6 + - - +
674D ARG* 5.4 0.5 + - - -
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Residues in contact with LEU 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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1007C ALA* 3.8 11.2 - - + -
1008C ARG 4.2 5.4 - - - +
625D TYR* 3.6 27.0 - - - +
626D SER* 3.5 44.0 - - - +
627D GLY 3.9 0.7 - - - +
644D LEU* 4.3 15.9 - - + -
648D MET* 2.9 42.9 + - + +
649D ALA* 3.9 7.4 - - - +
651D GLU* 1.3 78.9 - - - +
653D PHE* 1.3 63.1 + - + +
654D LYS 3.3 0.7 + - - -
655D PRO* 4.4 0.2 - - - +
656D PHE* 5.3 1.2 - - - -
747D VAL* 4.4 13.9 - - + +
749D VAL* 3.9 24.1 - - + +
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Residues in contact with PHE 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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644D LEU* 4.1 15.5 - - + -
649D ALA* 2.9 25.3 + - + +
650D LEU 4.0 1.3 - - - -
652D LEU* 1.3 77.5 - - + +
654D LYS* 1.3 64.3 + - - +
655D PRO* 3.4 5.2 - - - -
656D PHE* 2.8 30.4 + + - +
657D LEU* 3.1 9.2 + - - -
691D LEU* 4.2 7.0 - - + -
694D VAL* 4.1 19.5 - - + -
695D ILE* 3.7 33.0 - - + -
698D LYS* 4.5 22.0 - - + -
699D VAL 5.1 2.5 - - - -
700D VAL* 3.7 31.6 - - + -
718D PRO* 4.9 2.7 - - + -
749D VAL* 3.7 29.8 - - + -
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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