Contacts of the strand formed by residues 407 - 414 (chain A) in PDB entry 1UWV
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 THR 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A LEU* 3.9 6.7 - - - -
405A GLY 5.4 0.4 - - - +
406A TYR* 1.3 75.0 - - - +
408A ILE* 1.3 74.4 + - - +
409A ALA* 4.9 2.7 - - + +
429A PHE* 3.1 7.7 - - - -
430A SER* 2.9 46.4 + - - +
431A ARG 3.7 13.0 - - - +
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Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A MSE 3.8 43.3 - - + +
114A HIS* 3.9 34.5 - - + +
402A LEU* 4.1 20.7 - - + +
407A THR* 1.3 81.2 + - - +
409A ALA* 1.3 59.8 + - - +
410A ARG 3.9 20.6 - - - +
411A LEU* 4.6 4.3 - - + -
427A VAL* 4.0 6.7 - - + -
428A LEU 3.7 3.8 - - - -
429A PHE* 4.0 18.6 - - + -
1433A NI 3.6 20.4 - - - +
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Residues in contact with ALA 409 (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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114A HIS* 5.2 4.6 - - - -
117A SER* 4.7 0.9 + - - -
407A THR* 3.3 5.8 + - + +
408A ILE* 1.3 75.6 - - - +
410A ARG* 1.3 80.0 + - + +
428A LEU* 2.7 37.6 + - + +
430A SER* 4.1 18.6 - - - +
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Residues in contact with ARG 410 (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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114A HIS* 5.5 0.7 - - - -
117A SER* 3.6 21.1 - - - -
118A GLU* 4.8 3.6 - - - -
277A ARG* 4.3 14.8 - - - +
281A TRP* 3.7 34.3 - - + +
408A ILE* 3.6 3.9 - - - +
409A ALA* 1.3 98.6 + - - +
411A LEU* 1.3 60.2 + - - +
427A VAL* 3.3 10.4 - - - +
428A LEU* 2.9 42.1 + - + +
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Residues in contact with LEU 411 (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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108A LEU* 4.0 24.9 - - + +
112A MSE 3.9 28.3 - - + -
114A HIS* 3.6 22.4 - - + +
115A ASP 3.6 23.3 - - - +
116A VAL* 3.6 11.6 - - + -
117A SER* 2.7 41.3 + - - -
281A TRP* 4.1 1.6 - - - -
408A ILE* 4.6 4.7 - - + -
410A ARG* 1.3 76.6 - - - +
412A ALA* 1.3 64.8 + - - +
425A SER* 4.8 0.9 - - - -
426A MSE 3.5 3.4 - - - +
427A VAL* 3.4 30.3 - - + -
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Residues in contact with ALA 412 (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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108A LEU* 3.8 5.4 - - - +
116A VAL* 4.3 0.7 - - - -
118A GLU* 3.2 25.4 - - + +
120A ILE* 4.4 13.5 - - + -
281A TRP* 3.6 20.0 - - + -
411A LEU* 1.3 76.8 - - - +
413A MSE 1.3 59.9 + - - +
414A LEU* 4.4 8.7 - - + -
425A SER* 3.3 9.2 - - - -
426A MSE 2.8 32.2 + - + +
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Residues in contact with MSE 413 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLN* 4.9 5.8 - - - +
104A LYS* 4.0 23.8 - - + -
105A SER* 3.7 33.9 - - - +
108A LEU* 4.0 9.9 - - + -
116A VAL* 3.8 6.6 - - + +
118A GLU 3.0 5.7 + - - -
119A VAL* 3.3 15.3 - - + +
120A ILE 2.9 24.9 + - - -
412A ALA* 1.3 72.9 - - - +
414A LEU* 1.3 88.1 + - - +
415A ASP* 4.0 16.2 - - - +
422A HIS 4.5 1.6 - - - +
423A LEU* 3.7 31.9 - - + -
424A GLU 3.3 20.2 - - - +
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Residues in contact with LEU 414 (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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120A ILE* 3.6 41.1 - - + +
270A VAL* 4.8 2.2 - - + -
274A MSE 3.7 33.9 - - + -
387A VAL* 4.3 4.9 - - + -
412A ALA* 4.4 2.9 - - + -
413A MSE 1.3 87.7 - - - +
415A ASP* 1.4 56.4 + - - +
416A MSE 2.9 22.9 + - + -
424A GLU* 2.9 28.6 + - + +
425A SER* 3.8 32.5 - - - +
426A MSE 4.0 19.1 - - + -
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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