Contacts of the strand formed by residues 451 - 455 (chain A) in PDB entry 1GOG
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 SER 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A VAL* 3.6 2.9 - - - -
447A LEU* 2.9 42.4 + - - +
449A ASP* 2.6 32.2 + - - -
450A GLY* 1.3 81.9 - - - +
452A THR* 1.3 60.1 + - - +
475A ILE* 3.5 17.6 - - - +
476A TYR 3.2 17.3 - - - -
477A VAL* 4.5 9.0 - - - -
478A PRO* 3.9 4.4 - - - +
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Residues in contact with THR 452 (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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387A VAL* 3.7 40.7 - - + +
389A TYR* 4.1 12.8 - - - +
397A LEU* 3.8 25.0 - - + +
399A PHE* 3.9 17.3 - - + -
444A SER* 4.3 0.7 - - - -
445A VAL 3.5 9.0 - - - +
446A VAL* 4.4 0.3 - - - -
450A GLY 3.9 0.7 + - - -
451A SER* 1.3 76.9 + - - +
453A PHE* 1.3 63.6 + - - +
454A ILE* 3.9 7.6 - - + +
474A GLU 3.8 1.0 - - - +
475A ILE* 3.2 7.7 - - - -
476A TYR* 3.0 31.8 + - - -
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Residues in contact with PHE 453 (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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161A TRP* 4.0 7.4 - + - -
444A SER* 3.0 8.6 - - - -
445A VAL* 2.8 42.9 + - + +
447A LEU* 4.0 20.3 - - + +
451A SER 4.1 1.2 + - - -
452A THR* 1.3 72.5 - - - +
454A ILE* 1.4 59.5 + - - +
455A THR* 3.5 37.2 - - + -
473A PRO* 3.5 24.2 - - + -
474A GLU 3.7 2.7 - - - -
475A ILE* 3.9 15.3 - - + -
486A GLN* 4.7 1.6 - - + -
499A SER* 5.4 0.4 - - - -
507A VAL* 3.8 33.7 - - + -
528A PHE* 3.4 45.1 - + + -
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Residues in contact with ILE 454 (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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397A LEU* 5.0 1.1 - - + -
399A PHE* 3.6 48.0 - - + -
435A LEU* 4.0 8.5 - - + -
439A ARG* 3.9 20.1 + - - +
442A HIS* 3.7 15.9 - - + -
443A THR 3.4 4.0 - - - +
452A THR* 3.9 12.8 - - + +
453A PHE* 1.4 78.2 - - - +
455A THR* 1.3 66.4 + - - +
473A PRO* 3.2 6.1 - - - +
474A GLU* 2.8 42.4 + - + +
476A TYR 4.9 0.9 - - - +
483A PHE* 3.9 30.1 - - + -
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Residues in contact with THR 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TRP* 3.5 23.4 - - + -
439A ARG* 3.7 5.6 - - - +
442A HIS* 3.3 2.0 - - - +
443A THR* 2.8 40.4 + - - +
453A PHE* 3.5 24.9 - - + -
454A ILE* 1.3 80.3 - - - +
456A GLY* 1.3 67.4 + - - +
471A PHE 5.7 0.3 + - - -
473A PRO* 3.6 8.7 - - - +
489A ASN* 5.4 1.7 + - - -
497A SER* 5.6 0.3 + - - -
499A SER* 3.5 24.7 - - - +
509A ASN* 3.7 19.8 + - - +
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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