Contacts of the strand formed by residues 404 - 410 (chain A) in PDB entry 3UJK
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 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A THR 3.9 1.7 - - - +
117A SER* 3.4 1.4 + - - -
118A ILE* 2.9 48.1 + - + +
120A GLY* 5.4 0.2 - - - -
336A SER* 4.0 2.2 - - - -
338A GLY* 3.7 22.0 - - - +
339A LEU* 4.5 2.7 - - + +
392A SER* 4.1 18.9 + - - +
395A ALA* 4.0 16.6 - - + -
396A LEU* 3.8 33.9 - - + -
400A SER* 3.8 14.6 - - - +
402A ASP 3.4 9.6 + - - +
403A ASN* 1.3 79.0 - - - +
405A SER* 1.3 65.0 + - - +
406A VAL* 4.0 20.2 - - + -
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Residues in contact with SER 405 (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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116A THR 3.3 4.5 - - - -
117A SER* 2.8 20.9 + - - -
125A MET* 4.5 0.2 - - - +
127A ASP* 2.7 30.2 + - - +
129A VAL* 3.7 22.1 - - - +
163A VAL* 4.1 10.5 - - - -
334A LEU 4.5 0.2 - - - -
335A ALA* 3.1 9.2 - - - +
336A SER* 3.1 31.1 + - - +
404A ILE* 1.3 72.3 - - - +
406A VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 406 (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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115A VAL* 3.3 5.1 - - - +
116A THR* 2.8 54.0 + - + +
129A VAL* 5.3 0.2 - - - +
333A ILE* 3.8 17.9 - - + -
334A LEU 3.4 3.4 - - - +
335A ALA* 4.2 0.4 - - + -
339A LEU* 4.2 17.0 - - + -
388A ALA* 3.8 9.2 - - + +
391A LEU* 3.8 32.5 - - + -
392A SER* 4.6 1.6 - - - +
404A ILE* 4.0 17.9 - - + -
405A SER* 1.3 79.7 - - - +
407A VAL* 1.3 65.1 + - - +
408A VAL* 4.0 9.6 - - + -
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Residues in contact with VAL 407 (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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113A TYR* 5.1 0.9 - - + -
114A GLY 3.4 10.1 - - - +
115A VAL* 3.8 19.7 - - + -
129A VAL* 4.8 2.2 - - + -
130A SER 4.9 1.1 - - - +
131A THR* 4.0 11.4 - - + -
161A PHE* 3.8 35.7 - - + -
162A GLY 4.7 5.8 - - - +
163A VAL* 4.0 20.9 - - + -
332A LEU 3.7 0.9 - - - +
333A ILE* 3.3 5.4 - - - +
334A LEU* 2.8 43.2 + - + +
406A VAL* 1.3 75.7 - - - +
408A VAL* 1.3 64.0 + - - +
409A VAL* 4.2 10.1 - - + -
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Residues in contact with VAL 408 (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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113A TYR* 3.2 4.3 - - - +
114A GLY 2.9 32.5 + - - +
331A CYS* 4.4 9.2 - - + -
332A LEU 3.4 6.5 - - - +
333A ILE* 4.2 9.2 - - + -
352A ALA* 4.7 2.2 - - + -
356A ILE* 4.1 19.5 - - + -
384A ALA* 3.7 14.8 - - + +
387A ALA* 4.1 15.7 - - + -
388A ALA* 3.7 28.5 - - + +
391A LEU* 4.0 13.2 - - + -
406A VAL* 4.0 10.3 - - + -
407A VAL* 1.3 76.7 - - - +
409A VAL* 1.3 64.9 + - - +
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Residues in contact with VAL 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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111A PRO* 6.2 0.7 - - + -
112A LEU 3.4 14.1 - - - +
113A TYR* 4.2 1.6 - - + -
161A PHE* 3.8 49.6 - - + -
239A VAL* 4.8 8.7 - - + -
331A CYS* 3.2 8.2 - - - +
332A LEU* 2.8 54.2 + - + +
334A LEU* 6.2 0.9 - - + -
407A VAL* 4.2 5.4 - - + -
408A VAL* 1.3 77.1 - - - +
410A ASP* 1.3 68.3 + - - +
411A LEU* 3.5 16.6 + - + +
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Residues in contact with ASP 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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112A LEU* 2.8 47.8 + - + +
325A ARG* 4.8 1.4 + - - -
330A ASP 4.0 2.7 - - - -
331A CYS* 4.5 3.4 - - - -
356A ILE* 4.0 15.9 - - + +
360A HIS* 4.3 6.8 - - - -
381A ASP* 4.7 5.6 - - - +
384A ALA* 4.7 9.0 - - + +
408A VAL* 4.1 1.6 + - - +
409A VAL* 1.3 75.5 - - - +
411A LEU* 1.3 60.5 + - - +
412A LYS* 2.8 31.6 + - - +
415A ARG* 2.9 39.7 + - - -
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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