Contacts of the helix formed by residues 378 - 387 (chain B) in PDB entry 1UKW
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 PRO 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLN* 5.6 12.8 - - + +
286B ARG* 3.8 21.5 - - - +
290B GLU* 3.4 37.5 - - + +
368B HIS* 5.2 1.8 - - - +
376B GLU 4.8 0.9 - - - +
377B PHE* 1.3 95.2 - - + +
379B VAL* 1.3 64.5 + - - +
380B GLU 3.3 3.3 + - - -
381B LYS* 3.5 13.2 + - + +
382B LEU* 3.3 21.6 + - + +
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU* 3.9 14.6 - - + -
361B ALA 4.4 1.7 - - - +
364B ALA* 3.6 20.9 - - + -
365B ILE* 3.6 36.4 - - + +
368B HIS* 3.3 37.7 - - + +
372B GLY* 3.6 22.7 - - - +
377B PHE* 4.8 3.1 - - + -
378B PRO* 1.3 75.5 - - + +
380B GLU* 1.3 66.4 + - - +
382B LEU* 3.1 25.6 + - + +
383B LEU 3.5 3.8 + - - -
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Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ILE* 3.7 13.8 - - + +
372B GLY 3.4 16.6 - - - +
373B TYR* 4.3 18.2 - - + +
374B VAL 4.2 9.9 - - - +
375B ARG* 2.9 37.7 - - + +
377B PHE 4.4 2.9 + - - +
379B VAL* 1.3 79.9 - - - +
381B LYS* 1.3 72.4 + - - +
382B LEU 3.3 0.7 + - - -
383B LEU* 3.3 14.2 + - - +
384B ARG* 2.4 48.8 + - + +
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA* 3.9 20.6 - - + +
60B GLN* 5.0 7.9 - - + -
63B ASP* 3.5 35.0 - - + +
110B ALA 4.8 1.0 + - - -
111B CYS* 3.1 33.7 - - - +
234B GLN* 6.3 0.4 - - - +
235B ARG 6.3 0.2 - - - +
377B PHE 5.6 0.2 - - - +
378B PRO* 3.5 12.2 + - + +
379B VAL 3.3 0.4 - - - -
380B GLU* 1.3 81.7 + - - +
382B LEU* 1.3 67.0 + - + +
384B ARG* 3.3 26.7 + - - +
385B ASP* 2.8 62.9 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR 5.8 0.2 - - - +
110B ALA 5.9 0.7 - - - +
111B CYS* 6.5 0.7 - - - -
283B VAL* 4.0 19.2 - - + +
286B ARG* 4.0 27.8 - - + +
287B ALA* 3.9 34.1 - - + +
290B GLU* 4.9 2.5 - - + -
361B ALA* 3.9 12.3 - - + -
364B ALA* 5.3 0.2 - - + -
378B PRO* 3.3 15.3 - - + +
379B VAL* 3.1 28.6 + - + +
381B LYS* 1.3 85.7 - - + +
383B LEU* 1.3 56.6 + - - +
385B ASP* 3.3 8.1 + - - +
386B VAL* 2.9 34.0 + - - +
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Residues in contact with LEU 383 (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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232B MET* 5.5 0.2 - - - -
358B PHE* 3.4 52.8 - - + +
361B ALA* 3.6 6.6 - - + +
362B ASN* 3.8 22.2 - - + +
365B ILE* 3.8 24.2 - - + -
379B VAL 3.5 1.2 + - - -
380B GLU 3.3 10.6 + - - +
381B LYS 3.3 0.2 - - - -
382B LEU* 1.3 79.1 - - - +
384B ARG* 1.3 64.7 + - + +
386B VAL* 3.8 3.1 - - - +
387B LYS* 3.2 25.8 + - - +
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Residues in contact with ARG 384 (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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63B ASP* 3.1 37.6 + - - -
232B MET* 2.7 79.3 + - + +
233B GLY* 3.4 16.7 + - - -
235B ARG* 3.4 17.3 - - - +
375B ARG* 3.9 6.0 - - - +
380B GLU* 2.4 48.8 + - + +
381B LYS* 3.3 20.4 + - - +
383B LEU* 1.3 79.9 - - + +
385B ASP* 1.3 62.2 + - - +
387B LYS* 4.1 2.4 + - - +
388B LEU* 4.5 3.3 + - - +
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Residues in contact with ASP 385 (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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63B ASP* 4.6 1.4 - - - +
111B CYS* 5.1 0.2 - - - -
112B MET* 4.1 23.9 + - + -
113B GLY 4.2 2.2 + - - -
233B GLY* 3.6 4.3 - - - -
234B GLN* 2.9 49.1 + - + +
283B VAL* 5.6 1.6 - - + -
381B LYS* 2.8 58.7 + - - +
382B LEU* 3.6 8.2 - - - +
384B ARG* 1.3 77.7 - - - +
386B VAL* 1.3 65.4 + - - +
387B LYS 3.2 1.0 + - - -
388B LEU* 3.2 13.7 + - - +
389B ASN* 4.0 0.3 + - - -
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Residues in contact with VAL 386 (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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112B MET* 5.3 0.2 - - - -
280B SER* 4.5 2.2 - - - +
283B VAL* 3.9 24.0 - - + -
354B SER 4.6 2.6 - - - +
357B ALA* 3.4 32.5 - - + +
358B PHE* 3.4 38.4 - - + +
361B ALA* 4.6 0.9 - - + -
382B LEU 2.9 22.4 + - - +
383B LEU* 3.8 5.2 - - - +
385B ASP* 1.3 71.7 - - - +
387B LYS* 1.3 70.0 + - - +
389B ASN* 3.0 34.4 + - + +
390B GLN* 3.9 6.1 + - - +
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Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B MET* 3.7 31.9 - - + -
358B PHE* 3.9 28.5 - - + -
383B LEU 3.2 13.8 + - - +
384B ARG 4.3 0.7 - - - +
385B ASP 3.2 0.8 + - - -
386B VAL* 1.3 76.3 - - - +
388B LEU* 1.3 63.3 + - - +
390B GLN* 2.7 46.6 + - - +
391B ILE* 3.8 25.1 + - + +
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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