Contacts of the strand formed by residues 529 - 535 (chain H) in PDB entry 6V3O
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 PHE 529 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304H THR* 4.4 8.7 - - + -
308H CYS* 3.9 19.7 - - - -
452H LYS* 2.7 34.6 + - - -
453H LEU* 3.5 13.5 - - + +
455H ILE* 4.2 6.7 - - + -
521H LEU* 3.6 41.5 - - + -
524H LEU* 3.7 42.4 - - + -
525H PRO 3.9 7.6 - - - -
526H PRO* 3.2 12.5 + - + +
527H ASP 3.3 0.4 - - - -
528H SER* 1.3 91.9 - - - +
530H GLY* 1.3 60.5 + - - +
559H LEU* 3.7 35.2 - - + -
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Residues in contact with GLY 530 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452H LYS* 4.6 9.6 - - - -
453H LEU 2.9 15.3 + - - +
454H ASP* 4.1 3.8 - - - -
529H PHE* 1.3 76.8 - - - +
531H PRO* 1.3 71.8 - - - +
559H LEU* 3.4 22.7 - - - +
560H PRO* 3.9 8.2 - - - +
669H ARG* 5.7 0.4 - - - -
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Residues in contact with PRO 531 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454H ASP* 3.3 21.3 - - - +
455H ILE* 3.0 27.4 + - - +
530H GLY* 1.3 86.8 - - - +
532H TYR* 1.3 58.6 + - - +
533H ILE* 4.1 10.5 - - + -
559H LEU* 4.1 3.8 - - - +
560H PRO* 3.4 14.8 - - + +
562H VAL* 3.3 26.5 - - + -
596H GLN* 4.0 12.8 - - - +
669H ARG* 3.6 25.8 - - - +
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Residues in contact with TYR 532 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293H ARG* 5.8 1.0 - - - -
455H ILE* 3.5 30.1 - - + -
457H GLN* 3.6 17.4 - - + +
462H HIS* 2.8 40.1 + + - -
514H VAL* 4.8 2.6 - - - +
517H ALA* 5.8 6.3 - - + +
518H PHE* 3.4 35.3 - + - -
521H LEU* 4.1 12.8 - - + -
531H PRO* 1.3 71.2 - - - +
533H ILE* 1.3 73.5 + - - +
534H ILE* 4.3 2.9 - - + -
546H VAL* 3.8 22.9 - - + -
550H GLN* 5.2 3.4 - - - +
559H LEU* 4.1 13.1 - - + +
560H PRO 2.9 13.2 + - - +
561H VAL* 3.5 7.2 - - + +
562H VAL* 2.9 25.3 + - - +
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Residues in contact with ILE 533 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288H TRP* 4.0 15.5 - - + +
454H ASP* 4.0 19.5 - - + +
455H ILE 2.7 17.0 + - - +
456H ARG* 3.2 22.7 - - + +
457H GLN 3.0 26.0 + - - +
531H PRO* 4.1 9.6 - - + -
532H TYR* 1.3 80.3 - - - +
534H ILE* 1.3 64.1 + - - +
562H VAL* 3.3 24.7 - - + +
564H LEU* 4.1 12.6 - - + +
598H MET* 4.1 15.0 - - + -
638H PHE* 3.8 32.3 - - + -
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Residues in contact with ILE 534 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457H GLN 3.3 5.4 - - - +
459H SER* 3.6 38.8 - - - +
462H HIS* 4.1 7.6 - - + +
532H TYR* 4.3 3.1 - - + -
533H ILE* 1.3 75.2 - - - +
535H SER* 1.3 64.4 + - - +
537H ALA* 3.6 12.5 - - + +
542H ASP* 3.4 27.6 - - + +
543H VAL* 3.9 11.2 - - + +
546H VAL* 3.7 15.9 - - + -
561H VAL* 3.4 31.6 - - + -
562H VAL 2.9 13.8 + - - +
563H PRO* 5.0 0.7 - - + -
564H LEU* 2.9 28.5 + - - -
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Residues in contact with SER 535 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294H ASP* 3.5 27.8 - - - +
456H ARG* 3.1 35.3 + - - +
457H GLN 3.1 6.0 + - - -
458H GLU* 3.5 3.9 - - - -
459H SER 3.0 23.6 + - - -
533H ILE 3.9 0.6 + - - -
534H ILE* 1.3 72.2 - - - +
536H MET* 1.3 72.4 + - - +
564H LEU* 3.9 10.1 - - - +
566H GLU* 3.4 13.0 - - - -
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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