Contacts of the strand formed by residues 386 - 392 (chain A) in PDB entry 3I89
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 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A SER* 2.7 36.8 + - - -
384A GLU 3.8 5.8 - - - -
385A GLY* 1.4 77.6 - - - -
387A LEU* 1.3 64.3 + - - +
388A ARG* 3.1 30.7 + - - +
714A THR* 3.8 4.6 - - - +
715A VAL 3.6 9.0 - - - -
716A PRO* 4.0 6.3 - - - -
717A LEU* 3.5 21.7 - - - +
721A PRO* 3.4 13.0 - - - +
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Residues in contact with LEU 387 (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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376A VAL* 4.5 12.3 - - + -
377A THR 3.2 12.8 - - - +
378A CYS* 4.1 10.8 - - - -
386A SER* 1.3 77.7 + - - +
388A ARG* 1.3 64.6 + - - +
389A ILE* 4.5 2.0 - - + +
714A THR* 3.2 4.9 - - - +
715A VAL* 2.7 51.3 + - + +
717A LEU* 3.4 28.9 - - + -
721A PRO* 4.2 5.4 - - + -
724A ILE* 3.9 27.6 - - + -
733A PHE* 5.2 1.6 - - + -
735A VAL* 4.5 9.9 - - + -
794A ILE* 5.0 13.7 - - + -
799A PHE* 4.5 21.5 - - + -
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Residues in contact with ARG 388 (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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329A GLY* 5.1 1.8 - - - -
330A ASP* 2.6 47.6 + - - +
354A THR* 3.8 16.2 - - - +
355A ASN 3.7 16.3 + - - +
356A LEU* 3.9 27.2 - - + +
375A LEU 3.4 1.7 - - - +
376A VAL* 3.4 4.0 - - - -
377A THR* 3.0 42.0 + - - +
379A SER* 3.7 14.4 - - - +
384A GLU 4.7 6.9 + - - -
386A SER* 3.1 20.6 + - - +
387A LEU* 1.3 75.9 - - - +
389A ILE* 1.3 63.5 + - - +
390A ILE* 3.8 5.3 - - + +
712A ILE* 4.4 2.9 - - + -
713A ARG 3.1 6.3 - - - +
714A THR* 2.8 37.3 + - - +
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Residues in contact with ILE 389 (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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367A LEU* 4.1 13.9 - - + -
374A GLN* 3.1 31.4 - - + +
375A LEU 3.2 8.1 - - - +
376A VAL* 3.8 19.3 - - + -
387A LEU* 4.5 1.8 - - + +
388A ARG* 1.3 79.5 - - - +
390A ILE* 1.3 61.2 + - - +
391A ARG* 5.6 0.2 - - - -
711A HIS* 3.6 1.4 - - - +
712A ILE* 3.2 6.2 - - - +
713A ARG* 2.5 73.3 + - + +
715A VAL* 4.1 19.1 - - + -
799A PHE* 3.9 30.7 - - + -
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Residues in contact with ILE 390 (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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10A GLN* 6.0 0.2 - - - +
356A LEU* 4.2 20.6 - - + -
373A GLY 4.5 0.9 - - - +
374A GLN* 3.4 5.5 - - - -
375A LEU* 2.6 69.9 + - + +
377A THR* 4.1 14.8 - - + -
388A ARG* 3.8 24.2 - - + +
389A ILE* 1.3 74.2 - - - +
391A ARG* 1.3 63.0 + - - +
710A LEU* 4.6 21.3 - - + -
711A HIS 3.5 1.8 - - - +
712A ILE* 3.7 24.5 - - + -
1012A LEU* 4.5 9.3 - - + +
1037A ILE* 4.5 9.2 - - + -
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Residues in contact with ARG 391 (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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372A GLN* 4.0 12.8 - - - +
373A GLY 5.0 0.4 - - - +
374A GLN* 3.0 44.8 + - - +
389A ILE 5.6 0.2 - - - +
390A ILE* 1.3 76.3 - - - +
392A ASN* 1.3 88.0 + - - +
393A GLY 3.6 13.5 + - - -
395A GLY* 4.8 1.2 - - - -
672A ASN* 3.4 15.3 - - - +
705A ASP* 3.0 31.9 + - - +
710A LEU* 3.5 6.1 - - - -
711A HIS* 2.9 70.7 + - + +
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Residues in contact with ASN 392 (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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372A GLN* 6.0 2.6 - - + +
373A GLY 5.0 1.2 + - - -
390A ILE 4.4 0.2 - - - -
391A ARG* 1.3 92.3 - - - +
393A GLY* 1.3 70.4 + - - +
670A ASN* 4.3 9.1 - - - +
672A ASN* 3.0 11.0 + - - +
709A LYS* 3.1 52.7 + - - +
710A LEU* 3.9 9.6 - - - +
1012A LEU* 3.3 36.3 + - + +
1013A VAL* 3.6 19.7 - - + +
1140A HIS 3.8 4.0 - - - -
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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