Contacts of the strand formed by residues 428 - 432 (chain A) in PDB entry 3I5Y
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 GLY 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A TYR 2.8 10.4 + - - +
375A LYS* 3.3 2.5 - - - +
376A ALA 2.9 26.0 + - - +
401A LEU* 3.8 8.2 - - - +
402A PRO* 3.6 18.8 - - - -
404A LEU* 6.4 0.4 - - - -
422A PHE* 3.5 12.0 - - - -
427A SER* 1.3 76.0 - - - +
429A ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 3.7 40.8 - - + -
374A TYR* 4.9 2.7 - - + -
376A ALA* 3.3 17.9 - - + +
378A ILE* 3.8 28.7 - - + -
393A LEU* 4.3 5.4 - - + -
397A PHE* 4.8 5.4 - - + -
401A LEU* 4.0 16.6 - - + -
402A PRO 2.9 8.3 + - - +
403A ILE* 3.4 25.9 - - + +
404A LEU* 2.8 28.6 + - - +
422A PHE* 4.3 2.0 - - - -
428A GLY* 1.3 77.9 - - - +
430A LEU* 1.3 61.2 + - - +
431A VAL* 3.8 8.9 + - + -
449A LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 430 (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 ALA 3.0 6.6 + - - +
377A ILE* 3.4 15.2 - - + +
378A ILE* 2.8 28.8 + - - +
404A LEU* 3.7 19.7 - - + +
406A PHE* 3.6 38.8 - - + -
418A LEU* 3.6 19.7 - - + -
422A PHE* 3.8 29.6 - - + -
429A ILE* 1.3 72.2 - - - +
431A VAL* 1.3 59.7 + - - +
432A CYS* 4.0 4.5 - - - -
442A PHE* 3.6 36.6 - - + -
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Residues in contact with VAL 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ILE* 3.4 27.8 - - + +
380A ALA* 5.5 0.7 - - + -
386A THR* 3.7 22.5 - - + +
389A LEU* 4.1 18.4 - - + -
390A CYS* 3.4 30.7 - - - -
393A LEU* 3.6 17.5 - - + -
403A ILE* 3.9 7.6 - - + -
404A LEU 2.8 11.4 + - - +
405A GLU* 3.7 0.3 - - - -
406A PHE* 2.9 25.3 + - - +
429A ILE* 3.9 7.2 - - + -
430A LEU* 1.3 71.9 - - - +
432A CYS* 1.3 62.1 + - - +
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Residues in contact with CYS 432 (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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377A ILE* 3.9 18.2 - - - -
378A ILE 3.0 8.4 + - - -
379A PHE* 3.2 40.1 - - - -
380A ALA 2.9 24.4 + - - -
386A THR* 3.9 9.6 + - - -
406A PHE* 3.0 40.4 - - + +
430A LEU* 4.7 4.9 - - + -
431A VAL* 1.3 76.0 - - - +
433A THR* 1.3 66.3 + - - +
435A VAL* 4.7 0.2 - - + -
436A GLY* 4.7 3.6 - - - -
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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