Contacts of the helix formed by residues 660 - 671 (chain A) in PDB entry 1XJP
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 TYR 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A ASP* 5.2 5.0 + - - -
620A ARG 5.5 3.1 + - - -
622A TYR* 3.5 43.4 + + + +
629A PHE* 5.9 1.2 - - - -
659A SER* 1.4 87.5 + - - +
661A HIS* 1.3 58.5 + - + +
663A VAL* 3.1 25.5 + - + +
664A SER* 3.8 10.6 + - - -
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Residues in contact with HIS 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A CYS 4.6 3.6 - - - +
658A ALA* 2.6 27.2 + - + +
659A SER* 3.8 0.6 + - - -
660A TYR* 1.3 75.4 - - + +
662A THR* 1.3 53.2 + - - -
664A SER* 3.3 16.5 + - - +
665A LEU* 2.4 56.6 + - + +
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Residues in contact with THR 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PHE* 6.3 2.0 - - + -
256A TYR* 5.4 2.0 - - + -
257A LEU* 4.0 17.7 - - + -
324A PRO* 4.0 3.3 + - - +
442A TYR* 2.3 54.2 + - + +
658A ALA* 3.0 19.5 + - - +
659A SER 2.8 14.2 + - - -
661A HIS* 1.3 74.5 - - - +
663A VAL* 1.3 60.2 + - + +
665A LEU* 3.1 14.9 - - + +
666A LEU* 2.7 24.3 + - + +
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Residues in contact with VAL 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 2.2 65.7 - - + +
428A ILE* 4.3 13.9 - - + +
442A TYR* 5.2 0.2 - - - +
620A ARG* 4.7 8.7 - - + -
622A TYR* 3.3 21.5 - - + +
659A SER 4.7 5.8 - - - +
660A TYR* 3.1 17.2 + - + +
662A THR* 1.3 77.8 - - + +
664A SER* 1.4 58.6 + - - +
666A LEU* 3.2 8.8 + - + +
667A ARG* 3.0 22.7 + - - +
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Residues in contact with SER 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 5.0 4.6 - - - +
660A TYR* 3.8 11.8 + - - -
661A HIS* 3.3 24.2 + - - -
663A VAL* 1.4 77.7 - - - +
665A LEU* 1.3 59.1 + - - +
667A ARG* 3.2 32.7 + - - +
668A SER* 4.3 2.8 + - - -
672A LYS* 4.6 1.4 + - - -
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Residues in contact with LEU 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PHE* 5.3 11.8 - - + +
324A PRO* 6.1 0.2 - - + -
658A ALA* 4.4 14.1 - - + -
661A HIS* 2.4 56.5 - - + +
662A THR* 3.1 21.1 + - + +
664A SER* 1.3 75.9 - - - +
666A LEU* 1.4 60.2 + - - +
667A ARG 3.2 1.8 - - - -
668A SER* 2.9 25.5 + - - -
669A THR* 3.8 9.2 + - - +
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Residues in contact with LEU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PHE* 2.2 33.2 - - + +
254A VAL 3.0 11.7 - - - +
255A GLY 2.3 25.4 - - - +
256A TYR* 3.3 48.9 - - + +
257A LEU* 4.8 5.4 - - + -
428A ILE* 4.1 4.3 - - + -
662A THR* 2.7 12.3 + - + +
663A VAL* 3.2 20.6 + - + +
665A LEU* 1.4 71.2 - - - +
667A ARG* 1.4 51.9 + - - +
669A THR* 3.8 3.4 - - - -
670A SER* 2.7 54.2 + - - +
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Residues in contact with ARG 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A THR* 3.1 8.9 + - - -
428A ILE* 2.2 57.8 - - + +
429A ASP* 2.6 31.3 + - - -
617A PRO* 6.3 1.0 - - - +
619A TRP* 3.9 14.5 - - - -
663A VAL 3.0 7.9 + - - +
664A SER* 3.2 27.3 + - - +
666A LEU* 1.4 74.9 - - - +
668A SER* 1.3 52.8 + - - +
669A THR 3.1 5.5 + - - -
670A SER 3.7 1.6 + - - -
671A GLN 3.9 0.9 + - - -
672A LYS* 2.3 69.9 + - - +
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Residues in contact with SER 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A TRP* 5.1 13.6 - - - -
664A SER 4.3 2.7 + - - -
665A LEU* 2.9 18.4 + - - -
667A ARG* 1.3 76.7 - - - +
669A THR* 1.4 58.7 + - - +
672A LYS* 3.0 22.8 - - - +
673A SER* 2.7 35.2 + - - -
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Residues in contact with THR 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ALA* 5.1 6.3 - - + +
253A PHE* 2.8 48.1 + - + -
254A VAL* 3.3 17.1 - - - +
665A LEU 3.8 6.8 + - - +
666A LEU 3.3 4.4 + - - -
667A ARG 3.2 0.2 - - - -
668A SER* 1.4 93.1 - - - +
670A SER* 1.4 66.7 + - - +
671A GLN 3.4 2.1 + - - -
672A LYS 4.6 0.9 - - - -
673A SER* 4.3 14.2 + - - +
674A ILE* 5.2 5.0 - - - +
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Residues in contact with SER 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 6.3 2.0 - - - -
226A ILE* 5.6 0.2 - - - +
254A VAL* 2.2 48.8 + - - +
425A THR* 5.9 0.2 - - - -
427A ASN* 5.7 7.4 - - - -
428A ILE* 5.7 4.0 - - - -
666A LEU* 2.7 32.1 + - - +
667A ARG* 4.7 0.9 - - - -
669A THR* 1.4 76.8 + - - +
671A GLN* 1.4 77.0 + - - +
674A ILE* 3.7 13.1 - - - +
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Residues in contact with GLN 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLY 3.7 8.7 + - - -
226A ILE* 3.3 47.9 - - - +
423A TRP 4.1 0.5 - - - +
424A ASN 3.2 5.6 - - - +
425A THR* 3.5 28.9 - - + +
426A ARG* 3.6 22.7 - - - +
427A ASN* 4.0 12.4 + - + +
615A LEU* 4.8 12.5 - - + +
667A ARG 3.9 1.6 + - - -
670A SER* 1.4 89.8 + - - +
672A LYS* 1.3 66.8 + - - +
673A SER 3.7 1.3 - - - -
674A ILE* 3.6 24.5 + - - +
675A VAL* 4.0 6.2 + - - +
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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