Contacts of the helix formed by residues 498 - 505 (chain A) in PDB entry 5M64
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 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A GLY 4.3 0.4 - - - +
497A VAL* 1.3 89.8 - - + +
499A PRO* 1.3 66.6 - - + +
500A VAL* 3.2 18.2 - - + -
501A PHE* 3.2 14.5 + - + +
502A ALA* 3.0 23.1 + - - +
607A VAL* 5.6 0.2 - - - -
608A LEU* 4.3 4.0 - - + +
611A GLU 3.4 20.4 - - - +
612A LYS 3.1 22.0 - - - +
613A THR 3.3 20.9 - - - +
614A LEU* 4.1 15.3 - - + -
615A ARG* 5.0 0.7 - - - +
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Residues in contact with PRO 499 (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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497A VAL 3.9 0.9 - - - +
498A PRO* 1.3 86.9 - - + +
500A VAL* 1.3 58.8 + - + +
502A ALA* 3.5 10.7 - - + +
503A VAL* 2.9 33.3 + - - +
530A TRP* 5.4 12.3 - - + -
607A VAL* 5.8 4.0 - - + -
608A LEU 3.6 15.5 - - - +
609A PRO* 3.6 31.9 - - + -
611A GLU 4.6 4.5 - - - +
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Residues in contact with VAL 500 (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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498A PRO* 3.7 19.3 - - + -
499A PRO* 1.3 79.3 - - + +
501A PHE* 1.3 66.3 + - + +
503A VAL* 3.3 20.2 - - - +
504A LYS* 3.7 12.3 - - - +
611A GLU 5.1 0.4 - - - +
612A LYS* 3.8 19.7 - - + +
1044B PHE* 3.5 37.3 - - + -
1046B VAL* 4.7 0.9 - - - +
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Residues in contact with PHE 501 (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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480A ALA* 4.4 14.1 - - + -
481A ARG 4.5 4.7 - - - -
482A SER* 3.2 31.6 - - - -
497A VAL* 5.3 2.0 - - + -
498A PRO* 3.2 19.0 + - + +
500A VAL* 1.3 81.0 - - + +
502A ALA* 1.3 63.6 + - - +
503A VAL 3.4 0.7 - - - -
504A LYS* 3.6 1.5 + - - +
505A LEU* 3.3 29.9 + - + +
612A LYS 5.0 2.9 - - - -
614A LEU* 3.5 22.0 - - + -
635A MET* 4.8 12.3 - - + -
1044B PHE* 3.4 45.3 - + - -
1045B GLN 4.6 1.3 - - - -
1046B VAL* 3.5 42.4 - - + -
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Residues in contact with ALA 502 (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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497A VAL* 5.1 1.5 - - + +
498A PRO 3.0 15.7 + - - +
499A PRO* 3.1 11.8 + - + +
501A PHE* 1.3 75.9 - - - +
503A VAL* 1.3 59.8 + - - +
505A LEU* 2.9 23.7 - - - +
530A TRP* 4.6 9.9 - - + -
580A HIS* 3.2 15.3 - - - +
581A ILE* 3.6 37.2 - - + -
607A VAL* 4.8 6.1 - - + -
635A MET* 6.5 0.2 - - - -
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Residues in contact with VAL 503 (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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499A PRO 2.9 20.0 + - - +
500A VAL* 3.3 17.3 - - - +
502A ALA* 1.3 77.6 - - - +
504A LYS* 1.3 78.6 + - + +
505A LEU 4.2 0.3 - - - +
527A PRO* 3.3 31.4 - - + +
528A ASP 5.8 0.2 - - - -
530A TRP* 6.6 0.2 - - + -
534A THR* 3.6 19.6 - - + +
580A HIS* 4.0 19.8 - - + +
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Residues in contact with LYS 504 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A VAL 3.7 14.1 - - - +
501A PHE 3.6 2.6 + - - +
502A ALA 3.3 0.4 - - - -
503A VAL* 1.3 91.3 - - + +
505A LEU* 1.3 66.1 + - - +
506A THR* 3.5 5.4 + - - +
534A THR* 4.8 3.5 - - - +
1046B VAL* 3.8 32.5 - - + +
1047B ARG* 5.3 0.7 - - - +
1048B SER* 3.2 31.3 + - - +
1066B HIS* 5.8 9.8 - - + -
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Residues in contact with LEU 505 (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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478A TYR* 4.0 21.1 - - + +
479A ALA 3.9 4.9 - - - +
480A ALA* 4.2 16.2 - - + -
501A PHE 3.3 17.2 + - - +
502A ALA* 2.9 14.8 - - - +
503A VAL 4.2 0.7 - - - +
504A LYS* 1.3 78.1 - - - +
506A THR* 1.3 60.1 + - - +
580A HIS* 2.9 20.3 - - - +
581A ILE* 6.2 4.0 - - + -
635A MET* 3.7 33.4 - - + +
637A PHE* 4.5 23.1 - - + -
1046B VAL* 3.9 13.0 - - + -
1047B ARG 3.7 24.7 - - - +
1048B SER* 4.3 2.0 - - - -
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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