Contacts of the strand formed by residues 358 - 363 (chain A) in PDB entry 1B4V
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 VAL 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ILE 3.9 1.2 - - - +
350A ALA* 2.9 38.6 + - - +
351A TRP* 3.3 2.2 + - - -
356A SER 3.4 11.2 + - - +
357A SER* 1.3 82.0 - - - +
359A PHE* 1.3 66.0 + - - +
360A ALA* 3.9 3.8 - - + -
378A ALA* 4.0 26.2 - - + -
379A ILE 3.4 5.4 - - - +
380A THR* 4.1 6.5 - - + -
412A ALA 3.5 29.4 - - - +
413A ALA* 4.1 1.6 - - - +
416A LEU* 3.9 33.9 - - + -
417A PHE* 4.8 1.3 - - + -
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Residues in contact with PHE 359 (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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124A VAL* 4.6 17.9 - - + -
189A VAL* 5.4 11.4 - - + -
191A VAL* 5.0 17.3 - - + -
347A GLY* 5.2 9.4 - - - -
348A ILE 3.5 4.5 - - - -
349A ASP* 3.8 40.2 - - + -
351A TRP* 4.0 9.2 - - + -
358A VAL* 1.3 72.5 - - - +
360A ALA* 1.3 64.8 + - - +
361A GLU* 4.1 3.0 + - + -
377A LEU 3.9 0.5 - - - +
379A ILE* 2.9 42.7 + - + +
483A GLY 3.4 25.4 - - - +
484A VAL* 4.4 17.3 - - + -
485A ASN* 4.9 12.6 - - - -
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Residues in contact with ALA 360 (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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347A GLY* 3.2 3.8 - - - -
348A ILE* 2.7 51.6 + - + +
358A VAL* 3.9 8.2 - - + -
359A PHE* 1.3 75.2 - - - +
361A GLU* 1.3 64.3 + - - +
362A ILE 3.6 0.5 + - - -
376A TYR* 4.6 1.8 - - + -
377A LEU 3.5 8.7 - - - +
378A ALA* 4.1 8.1 - - - -
416A LEU* 4.9 0.7 - - + -
417A PHE* 3.7 30.1 - - + -
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Residues in contact with GLU 361 (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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122A MET* 3.3 40.9 - - - +
191A VAL* 6.3 1.3 - - + -
344A PRO* 3.2 25.3 - - + +
346A LEU 4.2 5.4 - - - +
347A GLY* 4.3 2.5 - - - -
359A PHE* 4.1 5.5 + - + -
360A ALA* 1.3 72.6 - - - +
362A ILE* 1.3 60.8 + - - +
363A ALA* 3.2 22.4 + - - +
364A PRO* 4.4 0.3 - - - +
376A TYR* 3.3 6.5 - - - +
377A LEU* 2.9 61.6 + - - +
379A ILE* 6.4 1.3 - - + -
447A HIS* 5.9 0.5 + - - -
485A ASN* 4.5 10.4 - - - +
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Residues in contact with ILE 362 (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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173A PHE* 3.6 19.8 - - + +
174A ALA* 4.0 24.0 - - + +
177A SER* 3.8 37.2 - - - +
178A ARG 4.5 0.2 - - - +
188A THR* 4.3 6.5 - - + -
344A PRO* 3.8 15.6 - - - +
345A ALA 5.0 0.5 + - - -
346A LEU* 3.2 45.8 + - + +
347A GLY* 4.3 1.8 - - - +
348A ILE* 4.2 23.1 - - + -
360A ALA 3.6 0.2 + - - -
361A GLU* 1.3 70.1 - - - +
363A ALA* 1.3 61.5 + - - +
374A SER* 6.2 0.7 - - - -
375A LEU 3.9 7.6 - - - +
376A TYR* 4.2 11.0 - - + -
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Residues in contact with ALA 363 (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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173A PHE* 3.8 7.1 - - - -
325A MET* 5.1 3.8 - - - -
340A GLN* 4.7 0.5 - - - +
361A GLU* 3.2 23.6 + - - +
362A ILE* 1.3 72.6 - - - +
364A PRO* 1.3 71.3 - - + +
365A MET* 4.0 1.4 + - - +
375A LEU* 2.9 55.7 + - + +
376A TYR* 4.4 2.2 - - - +
377A LEU* 4.7 2.9 - - + +
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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