Contacts of the strand formed by residues 427 - 431 (chain B) in PDB entry 5IZL
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 LEU 427 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B GLN* 4.4 28.9 + - + +
136B ILE* 3.2 35.4 - - + +
137B ALA* 4.7 8.5 - - + -
338B THR 4.0 8.4 - - - +
339B VAL* 4.0 6.2 - - - -
340B GLY 4.3 4.3 + - - -
426B CYS* 1.3 81.8 - - - +
428B VAL* 1.3 68.1 + - - +
429B ILE* 3.8 31.9 - - + -
448B GLY 3.7 10.1 - - - +
449B ILE* 4.6 4.9 - - + +
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Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 3.6 34.3 - - + -
337B ILE* 4.0 23.3 - - + -
338B THR 3.8 3.6 - - - +
339B VAL* 4.5 9.4 - - + -
414B VAL* 5.8 1.6 - - + -
427B LEU* 1.3 81.7 - - - +
429B ILE* 1.3 75.6 + - - +
446B PHE* 5.0 4.0 - - + -
447B HIS* 3.3 1.4 - - - +
448B GLY 2.9 34.1 + - - +
450B LEU* 3.9 37.0 - - + +
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Residues in contact with ILE 429 (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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104B ILE* 3.7 32.8 - - + -
133B ILE* 5.0 11.9 - - + -
136B ILE* 4.8 14.1 - - + -
322B ILE* 5.2 2.2 - - + -
336B HIS 3.9 0.2 - - - +
337B ILE* 3.4 5.7 - - - +
338B THR* 2.9 40.3 + - - +
427B LEU* 3.8 19.1 - - + -
428B VAL* 1.3 85.9 - - - +
430B GLY* 1.3 69.2 + - - +
431B SER* 4.7 2.6 + - - +
444B LEU* 4.5 24.5 - - + -
446B PHE* 3.6 12.8 - - - +
447B HIS* 4.1 9.9 - - + +
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Residues in contact with GLY 430 (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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335B PHE* 4.6 0.2 - - - -
336B HIS 3.2 9.0 - - - -
337B ILE* 4.5 2.5 - - - -
429B ILE* 1.3 75.3 - - - +
431B SER* 1.3 64.4 + - - -
444B LEU 3.7 0.5 - - - -
445B ALA* 2.8 22.8 + - - -
446B PHE* 3.2 46.0 + - - +
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Residues in contact with SER 431 (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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104B ILE* 5.1 2.1 - - - +
335B PHE* 4.0 5.9 - - - -
336B HIS* 2.9 38.4 + - - +
338B THR* 4.8 7.1 + - - -
429B ILE* 4.7 3.6 + - - +
430B GLY* 1.3 78.7 - - - -
432B ARG* 1.3 66.0 + - - +
433B LEU* 3.7 28.4 - - - +
443B ARG 3.2 15.9 - - - -
444B LEU* 3.8 16.3 - - - +
445B ALA* 3.9 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