Contacts of the strand formed by residues 364 - 370 (chain B) in PDB entry 3UAJ
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 364 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B ASN 5.0 2.4 - - - +
309B ASP* 3.5 35.7 - - + +
323B LYS* 3.8 43.7 - - + +
324B VAL 3.4 5.8 - - - +
325B LYS* 4.5 10.8 - - + -
362B ASN 4.7 3.8 - - - +
363B SER* 1.3 81.3 + - - +
365B THR* 1.3 64.5 + - - +
366B ASN* 4.5 1.7 + - - +
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Residues in contact with THR 365 (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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145B ASN* 4.4 8.7 - - - +
306B PHE* 5.8 1.9 - - - -
323B LYS* 3.4 4.5 - - - -
324B VAL* 3.0 35.0 + - - -
335B VAL* 5.1 3.6 - - + -
356B PRO* 4.0 17.5 - - + -
357B LEU 3.0 32.5 + - - +
358B ALA* 3.9 9.4 - - - +
363B SER* 4.4 4.7 + - - -
364B VAL* 1.3 75.8 + - - +
366B ASN* 1.3 66.9 + - - +
367B ILE* 3.4 24.6 - - + +
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Residues in contact with ASN 366 (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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101A TRP* 3.7 14.5 - - - -
1B MET* 3.8 32.0 - - + +
144B HIS 5.2 0.2 - - - -
145B ASN* 3.3 33.4 + - - +
321B VAL* 4.4 2.0 - - - +
322B VAL 3.8 2.0 - - - -
323B LYS* 2.8 48.4 + - - +
353B SER* 4.2 8.5 + - - -
356B PRO* 5.0 1.0 - - - +
364B VAL* 5.0 1.9 - - - +
365B THR* 1.3 75.9 - - - +
367B ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 367 (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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1B MET* 5.4 1.1 - - - -
320B THR 3.7 1.6 - - - +
321B VAL* 3.4 7.6 - - - +
322B VAL* 3.0 42.7 + - + +
324B VAL* 3.8 23.6 - - + -
335B VAL* 4.4 2.0 - - + -
337B ILE* 3.8 26.5 - - + -
351B ILE* 3.8 26.5 - - + -
353B SER* 4.0 3.4 - - - -
356B PRO* 3.7 25.8 - - + -
365B THR* 3.4 34.1 - - + +
366B ASN* 1.3 75.8 - - - +
368B GLU* 1.3 60.9 + - - +
369B LEU* 3.8 12.7 + - + +
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Residues in contact with GLU 368 (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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1B MET* 5.0 3.3 - - - -
4B VAL* 3.7 10.4 - - - +
9B ARG* 2.8 45.5 + - - -
11B PHE* 4.4 2.0 - - - -
144B HIS* 3.3 15.9 - - + +
315B THR* 4.6 1.0 - - - +
319B THR* 3.0 20.6 + - - +
320B THR 3.4 3.8 - - - +
321B VAL* 4.0 16.9 - - + +
351B ILE* 3.7 5.0 - - - +
352B ILE* 2.8 54.3 + - + +
353B SER* 3.2 20.1 + - - +
367B ILE* 1.3 71.7 - - - +
369B LEU* 1.3 55.5 + - - +
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Residues in contact with LEU 369 (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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312B MET* 3.9 17.7 - - - -
319B THR* 3.4 5.7 - - - -
320B THR* 2.7 48.7 + - - +
322B VAL* 3.9 27.6 - - + -
337B ILE* 3.7 26.5 - - + -
339B ILE* 3.8 14.6 - - + -
350B ARG 4.0 2.5 - - - -
351B ILE* 3.8 21.8 - - + -
352B ILE* 3.5 4.9 - - - -
367B ILE* 3.8 16.2 - - + +
368B GLU* 1.3 74.6 - - - +
370B GLU* 1.3 57.7 + - - +
371B PRO* 3.7 2.0 - - + -
378B ILE* 3.9 18.8 - - + -
380B ILE* 5.6 0.2 - - + -
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Residues in contact with GLU 370 (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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11B PHE* 6.1 1.2 - - - -
319B THR* 4.3 18.6 - - + +
339B ILE* 4.3 2.5 - - - -
349B GLY* 3.8 4.2 - - - -
350B ARG* 2.8 81.1 + - + +
352B ILE* 3.8 12.5 - - + +
369B LEU* 1.3 73.3 - - - +
371B PRO* 1.4 63.1 - - - +
372B PRO 3.9 0.2 - - - -
393B ARG* 4.2 18.8 + - - +
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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