Contacts of the helix formed by residues 648 - 656 (chain D) in PDB entry 1XFV
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 PRO 648 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628D PHE* 5.3 0.9 - - + -
646D THR 3.6 8.7 - - - +
647D ASP* 1.3 85.1 - - - +
649D ILE* 1.3 59.5 + - + +
651D LYS* 2.6 40.1 + - + +
652D ALA 3.6 1.7 + - - -
90R ARG* 4.3 17.9 - - + +
93R ASP* 3.3 26.5 - - - +
96R GLY* 4.2 19.5 - - - +
98R GLY* 3.9 13.3 - - - +
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Residues in contact with ILE 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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647D ASP* 3.2 15.7 + - - +
648D PRO* 1.3 76.7 - - + +
650D THR* 1.3 64.2 + - - +
652D ALA* 3.1 14.6 + - - +
653D LYS* 3.6 7.6 + - - +
86R ARG* 3.9 30.7 - - + +
89R PHE* 3.5 32.8 - - + -
90R ARG* 4.3 7.2 - - + +
98R GLY* 4.2 9.6 - - - +
138R TYR* 3.5 44.4 - - + +
139R GLU* 5.4 4.0 - - - +
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Residues in contact with THR 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D ASP* 3.4 28.7 + - + +
648D PRO 3.1 0.6 - - - -
649D ILE* 1.3 73.8 - - - +
651D LYS* 1.3 56.9 + - - +
652D ALA 3.0 11.0 + - - -
653D LYS* 3.2 31.4 + - + +
654D ILE* 4.5 8.9 - - + +
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Residues in contact with LYS 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 THR* 5.9 9.6 - - + -
647D ASP 3.3 11.0 + - - +
648D PRO* 2.6 26.0 + - + +
650D THR* 1.3 70.5 - - - +
652D ALA* 1.3 55.8 + - - +
653D LYS 3.7 0.2 - - - -
654D ILE* 4.5 10.3 - - - +
96R GLY 4.0 20.6 + - - +
97R ASN* 5.8 2.6 - - - +
98R GLY 5.8 0.9 - - - +
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Residues in contact with ALA 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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649D ILE 3.1 10.4 + - - +
650D THR 3.0 0.8 - - - -
651D LYS* 1.3 80.0 - - - +
653D LYS* 1.3 57.5 + - - +
654D ILE* 3.2 4.0 - - - +
655D ASN* 3.4 11.9 + - - +
656D THR* 2.7 26.7 + - - -
97R ASN 4.3 9.0 - - - +
98R GLY* 4.4 9.2 - - - +
99R TYR* 3.7 32.3 + - + +
137R ASN* 6.3 0.7 - - + -
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Residues in contact with LYS 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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649D ILE 3.6 4.2 + - - +
650D THR* 3.2 30.5 + - + +
652D ALA* 1.3 78.6 - - - +
654D ILE* 1.3 58.4 + - + +
655D ASN 2.8 12.2 + - - -
656D THR* 2.9 19.8 + - - -
662D GLU* 3.3 23.4 + - - +
751D TYR* 3.6 11.2 - - - +
755D ARG* 3.2 52.0 - - - +
139R GLU* 4.7 9.1 + - - -
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Residues in contact with ILE 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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650D THR 4.5 10.8 - - - +
651D LYS* 4.5 13.5 - - - +
652D ALA* 4.8 0.7 - - - -
653D LYS* 1.3 81.6 - - + +
655D ASN* 1.3 76.9 + - - +
656D THR 3.6 0.4 - - - -
751D TYR* 5.9 8.1 - - + +
754D GLU* 4.6 10.0 - - + +
755D ARG* 3.9 15.2 - - - +
758D ASN* 2.9 29.4 + - - +
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Residues in contact with ASN 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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652D ALA* 3.4 9.0 + - - +
653D LYS 2.8 4.4 + - - -
654D ILE* 1.3 100.6 + - - +
656D THR* 1.3 55.2 + - - +
758D ASN* 3.6 31.1 - - + +
759D GLN* 2.7 29.2 - - - +
762D LEU* 4.7 13.1 - - + +
99R TYR* 3.9 14.8 + - - +
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Residues in contact with THR 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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652D ALA 2.7 25.3 + - - -
653D LYS* 2.9 16.5 + - - -
654D ILE 3.6 1.2 + - - -
655D ASN* 1.3 73.1 + - - +
657D ILE* 1.3 61.8 + - - +
658D PRO* 2.9 1.3 - - + +
705D TYR* 3.0 27.8 - - - +
755D ARG* 2.8 44.7 + - - +
759D GLN* 3.4 11.7 + - - +
99R TYR* 4.5 4.0 + - - -
137R ASN* 4.8 10.0 + - - +
139R GLU* 3.8 23.1 + - + +
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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