Contacts of the strand formed by residues 443 - 447 (chain A) in PDB entry 3G1Q
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 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A MET* 3.8 24.7 + - + +
158A TRP* 2.6 51.7 + + + +
320A ARG* 2.9 19.1 + - - -
439A ALA 2.8 24.5 + - - +
440A PHE* 3.5 8.0 - - - -
442A SER* 1.3 90.6 - - - +
444A ASP* 1.3 61.4 - - - +
445A PHE* 3.6 15.9 - - + -
473A TYR* 3.5 37.9 - + + -
474A ILE 3.3 12.8 - - - +
475A ARG* 2.7 33.1 + - - -
476A ARG* 3.6 7.5 - - - +
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 4.3 8.8 - - - +
320A ARG* 2.7 32.3 + - - +
440A PHE* 5.0 1.0 - - - -
443A TYR* 1.3 74.1 - - - +
445A PHE* 1.3 68.0 + - - +
446A GLN* 6.2 0.2 - - + -
473A TYR* 3.4 3.8 - - - -
474A ILE* 2.8 50.1 + - + +
476A ARG* 2.9 30.3 + - - +
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Residues in contact with PHE 445 (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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158A TRP* 3.5 31.9 - + - -
165A ILE* 4.7 3.6 - - + -
167A LEU* 5.0 0.7 - - + -
304A MET* 3.5 27.8 - - + -
308A MET* 3.3 46.2 - - + +
439A ALA* 4.1 8.7 - - + -
440A PHE* 3.5 27.4 - + - -
443A TYR* 3.6 24.5 - - + -
444A ASP* 1.3 78.5 + - - +
446A GLN* 1.3 69.9 + - - +
471A VAL* 3.8 18.8 - - + -
472A LYS 3.2 4.9 - - - +
473A TYR* 3.8 21.5 - - + -
474A ILE* 4.7 0.2 - - - -
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Residues in contact with GLN 446 (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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308A MET* 3.9 6.7 - - - -
444A ASP* 6.2 0.4 - - + -
445A PHE* 1.3 80.2 - - - +
447A LEU* 1.3 68.2 + - - +
448A LEU* 3.6 2.7 + - + +
471A VAL* 3.6 2.6 - - - -
472A LYS* 2.8 61.2 + - + +
474A ILE* 3.7 22.4 - - + +
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Residues in contact with LEU 447 (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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305A LEU* 3.7 30.5 - - + +
308A MET* 3.7 22.5 + - + +
309A HIS* 3.4 41.3 - - + +
310A PRO* 5.1 3.6 - - + -
446A GLN* 1.3 77.5 - - - +
448A LEU* 1.3 62.1 + - - +
449A ARG* 3.2 26.7 + - + +
451A GLU 4.0 3.4 - - - +
452A VAL* 4.0 16.4 - - + +
453A PRO* 4.4 12.8 - - + -
468A GLN 5.3 3.1 - - - +
470A ARG 5.3 1.3 - - - +
471A VAL* 4.4 6.5 - - + -
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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