Contacts of the strand formed by residues 498 - 502 (chain A) in PDB entry 3HIG
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 GLY 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A GLY 3.2 7.0 + - - -
495A LEU* 3.3 22.4 + - - +
496A ARG 3.7 1.0 - - - -
497A HIS* 1.3 81.8 - - - +
499A THR* 1.3 63.1 + - - -
506A ILE* 4.2 4.7 - - - -
507A GLY 3.1 15.0 - - - -
509A ILE* 3.9 4.9 - - - -
676A ILE* 5.7 0.7 - - - -
677A PRO* 5.3 0.7 - - - -
554B LEU* 3.6 19.0 - - - +
589B HIS* 4.7 2.3 - - - -
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Residues in contact with THR 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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498A GLY* 1.3 77.2 + - - -
500A ARG* 1.3 71.0 + - - +
501A LEU* 3.3 10.7 + - + +
506A ILE* 3.4 5.3 - - - +
507A GLY 2.8 30.5 + - - -
676A ILE* 3.6 14.4 - - - +
677A PRO 2.7 32.0 + - - +
554B LEU* 4.5 2.3 - - - +
589B HIS* 3.4 29.4 - - + +
699B PHE* 5.1 0.7 - - - -
700B ASN* 3.9 17.8 + - - +
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Residues in contact with ARG 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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490A TYR* 3.4 44.8 + - + -
495A LEU* 3.8 11.1 - - + +
499A THR* 1.3 71.2 - - - +
501A LEU* 1.3 61.4 + - - +
502A HIS 3.3 23.4 + - - +
503A THR* 2.8 34.4 + - - +
505A LEU 3.4 8.5 - - - +
506A ILE* 3.7 6.1 - - - +
679A SER* 5.4 0.3 - - - -
587B TRP* 3.3 44.4 + - + +
589B HIS* 2.9 25.2 + - - +
700B ASN* 5.2 1.2 - - - +
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Residues in contact with LEU 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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485A VAL* 4.2 12.3 - - + -
499A THR* 3.4 21.3 - - + +
500A ARG* 1.3 78.6 - - - +
502A HIS* 1.3 66.1 + - - +
505A LEU* 2.9 16.1 + - + +
506A ILE 4.6 0.7 - - - -
507A GLY* 3.7 25.1 - - - +
677A PRO* 4.0 9.6 - - + -
678A HIS* 3.4 41.1 - - - +
679A SER* 3.7 4.3 - - - +
681A ASP* 5.0 2.5 - - + -
682A ILE* 3.9 38.9 - - + +
587B TRP* 3.4 23.6 + - - -
703B PRO 4.6 1.4 - - - +
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Residues in contact with HIS 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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282A PHE* 3.5 55.1 - + + +
500A ARG* 3.3 19.5 - - - +
501A LEU* 1.3 78.6 - - - +
503A THR* 1.3 91.9 + - - +
504A HIS 3.3 3.3 + - - +
505A LEU* 3.4 28.4 + - + +
682A ILE* 5.3 3.1 - - + -
587B TRP* 3.5 35.0 - + - -
704B GLU* 6.1 0.2 - - - -
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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