Contacts of the strand formed by residues 382 - 388 (chain B) in PDB entry 1F0C
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 ILE 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A MET* 3.0 37.2 - - + -
54A PRO* 4.4 9.2 - - + +
55A PRO* 3.2 22.7 - - - +
269A ASP* 4.1 14.6 - - - +
272A PHE* 4.4 14.8 - - + -
373B VAL* 4.1 13.9 - - + -
374B ILE 4.0 2.9 - - - -
375B ARG* 4.1 4.3 - - + -
380B GLY 3.3 8.7 + - - +
381B LYS* 1.3 78.3 - - - +
383B LEU* 1.3 61.7 + - - +
384B PHE 3.9 11.4 - - - +
385B VAL* 3.8 26.9 - - + -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 3.1 24.9 + - - -
54A PRO* 4.2 0.7 - - - -
55A PRO* 3.4 10.8 - - - +
112A PHE* 3.9 40.7 - - + -
190A PHE* 4.4 8.3 - - + -
248A THR* 4.1 14.8 - - + -
374B ILE* 2.8 16.9 + - + +
375B ARG 4.4 2.2 - - - -
376B HIS* 3.6 36.6 - - + +
381B LYS* 3.9 28.3 - - + +
382B ILE* 1.3 79.7 - - - +
384B PHE* 1.3 75.5 + - + +
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Residues in contact with PHE 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.4 34.5 - + + -
52A ILE 3.4 7.0 - - - +
53A SER* 3.5 29.6 - - - -
54A PRO* 4.0 1.6 - - - -
112A PHE* 3.8 26.0 - + - -
188A VAL* 4.0 11.4 - - + -
190A PHE* 3.6 28.3 - + + -
347A ALA* 4.0 21.8 - - + -
348A ALA 4.2 11.2 - - - -
349A ALA* 4.3 0.4 - - + -
372B TYR 4.8 0.4 - - - -
373B VAL* 3.4 6.4 - - - +
374B ILE* 2.8 51.5 + - + +
382B ILE* 3.7 0.8 - - - +
383B LEU* 1.3 81.6 - - + +
385B VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A MET* 3.5 32.8 - - + -
38A PHE* 3.9 35.0 - - + -
51A PHE* 3.6 4.4 - - - -
52A ILE* 2.9 33.6 + - + +
54A PRO* 3.6 21.5 - - + -
267A LEU* 4.2 4.0 - - + -
371B ILE* 4.6 0.9 - - + -
372B TYR 3.6 3.6 - - - +
373B VAL* 4.0 19.7 - - + -
382B ILE* 3.8 7.9 - - + -
384B PHE* 1.3 77.7 - - - +
386B GLY* 1.3 62.6 + - - +
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Residues in contact with GLY 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.8 7.4 - - - -
50A VAL 3.0 13.5 - - - -
51A PHE* 3.9 3.9 - - - -
371B ILE* 3.4 10.2 - - - +
372B TYR* 3.0 49.4 + - - +
385B VAL* 1.3 77.2 - - - +
387B ARG* 1.3 60.3 + - - +
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Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.7 13.2 - - + -
42A ALA* 3.5 26.3 + - - +
43A SER* 5.3 0.2 - - - +
45A MET 3.1 23.0 + - - -
46A LYS* 4.9 4.2 - - - +
47A GLY 3.9 3.7 - - - +
48A GLU 2.7 32.9 + - - +
49A ASN* 3.6 6.2 - - - +
50A VAL* 2.7 36.1 + - + +
260A LEU* 3.6 23.6 - - + -
264A GLU* 2.7 45.8 + - - +
360A DTT 4.9 7.9 - - - +
370B PHE 3.5 4.0 - - - -
371B ILE* 4.4 2.5 - - + +
372B TYR* 3.6 6.4 + - - -
386B GLY* 1.3 75.1 - - - -
388B TYR* 1.3 61.9 + - - +
389B CYS* 3.2 16.7 - - - -
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Residues in contact with TYR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASN* 3.8 2.9 - - - -
208A PHE* 3.4 34.8 - + - -
218A VAL* 3.5 13.2 - - - +
289A PRO* 3.9 14.1 - - + +
290A LYS 5.2 0.7 + - - -
291A PHE* 3.6 52.6 - + + +
293A VAL* 5.5 4.7 - - + -
369B PRO* 3.2 25.1 - - - +
370B PHE* 2.8 41.5 + + + +
372B TYR* 3.8 6.2 - - + -
387B ARG* 1.3 72.7 - - - +
389B CYS* 1.3 58.8 + - - +
390B SER 3.8 23.8 - - - -
391B PRO* 3.4 25.2 - - + +
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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