Contacts of the strand formed by residues 381 - 388 (chain C) in PDB entry 3IFS
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 ASN 381 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C ASP 4.7 2.3 - - - +
9C TYR* 5.0 0.2 - - - -
11C LYS* 4.1 8.6 + - + +
12C ALA* 3.7 23.7 + - - +
327C GLU* 3.4 34.6 + - - +
329C VAL* 3.8 12.7 - - + +
371C LEU* 3.8 40.9 - - + +
374C HIS* 3.8 11.6 + - - +
375C SER* 3.9 10.3 + - - +
379C VAL 2.8 26.9 + - - -
380C PRO* 1.3 74.3 + - - +
382C LEU* 1.3 64.6 + - - +
383C ILE* 4.4 1.6 + - - +
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Residues in contact with LEU 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 4.0 19.5 - - + -
8C ASP 3.9 2.5 - - - -
9C TYR* 3.9 14.4 - - + -
12C ALA* 3.9 18.2 - - + -
254C TYR* 4.3 9.4 - - + -
257C VAL* 3.7 34.1 - - + -
258C ARG 5.2 0.9 - - - +
261C LEU* 4.6 4.9 - - + -
326C PHE* 3.9 21.1 - - + -
327C GLU 2.8 13.2 + - - +
328C THR* 3.3 20.1 - - - +
329C VAL* 2.8 33.9 + - - +
381C ASN* 1.3 81.4 - - - +
383C ILE* 1.3 58.8 + - - +
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Residues in contact with ILE 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C THR 3.8 0.7 - - - +
7C PHE* 3.4 7.7 - - - -
8C ASP* 2.9 56.5 + - + +
11C LYS* 4.0 23.1 - - + +
329C VAL* 3.6 9.2 - - + +
331C LYS* 4.3 4.5 - - + -
367C TYR* 3.1 35.4 - - + +
371C LEU* 3.6 24.7 - - + -
381C ASN 4.8 1.8 - - - +
382C LEU* 1.3 81.3 - - - +
384C VAL* 1.3 67.1 + - - +
385C ASN* 3.5 28.9 - - - +
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Residues in contact with VAL 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C VAL* 3.6 25.8 - - + -
6C THR 3.4 4.0 - - - +
7C PHE* 4.2 10.5 - - + -
254C TYR* 5.6 0.9 - - + -
328C THR* 4.0 23.8 - - + -
329C VAL 2.9 8.7 + - - +
330C LEU* 3.5 14.8 - - + -
331C LYS 3.0 24.4 + - - -
383C ILE* 1.3 76.5 - - - +
385C ASN* 1.3 64.9 + - - +
386C ILE* 3.6 3.5 + - + +
397C LEU* 4.0 17.5 - - + -
400C PHE* 4.2 23.1 - - + -
401C PHE* 4.3 7.2 - - + -
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Residues in contact with ASN 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C HIS 4.3 1.0 - - - +
5C VAL* 3.2 11.8 - - - +
6C THR* 2.8 50.4 + - - +
8C ASP* 4.3 16.6 + - - +
331C LYS* 3.6 19.2 - - - +
367C TYR* 4.9 0.7 + - - -
383C ILE* 3.5 24.3 - - - +
384C VAL* 1.3 71.6 - - - +
386C ILE* 1.3 61.4 + - - +
387C PRO* 3.7 2.5 - - + +
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Residues in contact with ILE 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C VAL* 4.6 2.0 - - + -
278C LEU* 4.8 5.6 - - + -
330C LEU* 4.0 29.2 - - + -
331C LYS 2.8 11.7 + - - +
332C VAL* 3.2 14.6 - - + -
333C GLY 2.8 24.4 + - - -
384C VAL* 4.0 7.9 - - + +
385C ASN* 1.3 75.5 - - - +
387C PRO* 1.4 64.6 - - - +
388C GLU 3.3 10.4 + - - +
389C LEU* 4.1 17.5 - - + -
393C THR* 3.4 27.6 - - + -
397C LEU* 3.6 39.0 - - + -
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Residues in contact with PRO 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C THR* 3.4 43.3 - - + +
4C HIS 3.2 26.9 - - - +
5C VAL* 4.1 8.5 - - + -
333C GLY* 3.4 6.0 - - - +
334C LYS* 2.9 29.3 + - - +
385C ASN* 3.7 4.7 - - + +
386C ILE* 1.4 84.5 - - + +
388C GLU* 1.3 66.1 + - + +
393C THR* 4.4 5.4 - - + +
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Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C THR 5.3 7.5 + - - +
332C VAL* 4.4 1.8 - - - -
334C LYS* 4.3 24.1 - - + +
386C ILE* 3.3 5.5 + - - -
387C PRO* 1.3 86.7 - - + +
389C LEU* 1.3 61.3 + - - +
390C ASN* 3.3 28.3 + - - +
393C THR* 3.2 32.1 + - - +
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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