Contacts of the helix formed by residues 392 - 401 (chain A) in PDB entry 3UGM
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 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A GLY 3.5 5.4 + - - -
391A LEU* 1.3 72.1 - - - +
393A PRO* 1.3 62.5 - - + +
394A ASP* 3.0 21.5 - - + +
395A GLN* 2.7 60.3 + - - +
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Residues in contact with PRO 393 (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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355A HIS 5.8 1.8 - - - +
357A LEU* 4.9 9.8 - - + +
382A LEU* 4.9 12.9 - - + +
386A CYS* 4.3 8.3 - - - -
391A LEU 2.8 11.7 - - - +
392A THR* 1.3 86.8 - - + +
394A ASP* 1.3 65.4 + - - +
395A GLN 3.3 0.2 - - - -
396A VAL* 3.8 11.7 - - + +
397A VAL* 3.0 29.1 + - - +
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Residues in contact with ASP 394 (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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361A GLN* 3.9 19.6 + - - +
392A THR* 3.7 20.1 - - + +
393A PRO* 1.3 81.6 - - - +
395A GLN* 1.3 65.2 + - - +
397A VAL* 3.5 10.7 + - - +
398A ALA* 3.1 23.0 + - - +
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Residues in contact with GLN 395 (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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390A GLY 4.4 1.0 - - - +
391A LEU* 2.8 35.6 - - + +
392A THR* 2.7 44.0 + - - +
394A ASP* 1.3 76.9 - - + +
396A VAL* 1.3 53.7 + - - -
398A ALA* 2.9 10.9 + - - +
399A ILE* 2.8 26.4 + - - +
427A PRO* 4.9 6.9 - - - +
428A ASP* 3.9 31.1 + - - +
431A VAL* 4.1 22.7 - - + +
435A SER* 5.3 0.3 + - - -
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Residues in contact with VAL 396 (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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378A VAL* 5.5 1.4 - - - +
381A LEU 6.0 0.2 - - - +
382A LEU* 4.2 23.1 - - + +
385A LEU* 5.2 6.5 - - + -
391A LEU* 2.7 47.9 - - + +
392A THR 4.1 0.7 - - - +
393A PRO* 3.8 12.6 - - + +
395A GLN* 1.3 72.0 - - - +
397A VAL* 1.3 67.7 + - + +
399A ILE* 3.5 21.0 - - + +
400A ALA* 3.1 21.5 + - - +
409A LEU* 3.8 26.1 - - + +
412A VAL* 5.7 2.7 - - + -
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Residues in contact with VAL 397 (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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357A LEU* 4.4 19.7 - - + -
361A GLN* 3.1 62.1 - - + +
364A ALA* 5.3 1.1 - - + -
365A ILE* 4.3 10.6 - - + +
378A VAL* 6.2 1.6 - - - -
382A LEU* 6.5 0.2 - - + -
393A PRO 3.0 26.0 + - - +
394A ASP* 3.7 9.4 - - - +
395A GLN 3.2 1.0 - - - -
396A VAL* 1.3 76.2 - - + +
398A ALA* 1.3 59.7 + - + +
400A ALA* 3.0 8.0 + - - +
401A SER* 3.0 29.2 + - - +
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Residues in contact with ALA 398 (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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394A ASP 3.1 11.9 + - - +
395A GLN* 2.9 10.9 + - - +
397A VAL* 1.3 74.8 - - + +
399A ILE* 1.3 57.5 + - - +
400A ALA 3.2 0.9 - - - -
401A SER* 3.9 11.9 - - - -
402A HIS* 3.2 13.5 + - - -
435A SER* 3.0 23.9 - - - +
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Residues in contact with ILE 399 (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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391A LEU* 4.8 1.1 - - + -
395A GLN 2.8 8.9 + - - +
396A VAL* 3.6 25.4 - - + -
397A VAL 3.2 0.6 - - - -
398A ALA* 1.3 75.9 - - - +
400A ALA* 1.3 57.4 + - - +
401A SER 3.5 0.4 - - - -
402A HIS* 4.3 8.4 + - - +
405A GLY* 4.6 2.8 - - - -
408A ALA* 3.9 23.4 - - + +
409A LEU* 3.6 33.0 - - + +
412A VAL* 3.6 29.4 - - + -
431A VAL* 4.0 38.8 - - + +
434A ALA* 4.1 7.1 - - + +
435A SER* 4.0 11.0 - - - +
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Residues in contact with ALA 400 (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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365A ILE* 4.0 17.8 - - + +
374A ALA* 4.0 18.4 - - + +
378A VAL* 4.3 22.2 - - + -
396A VAL 3.1 14.5 + - - +
397A VAL* 3.0 6.8 + - - +
399A ILE* 1.3 82.6 - - + +
401A SER* 1.3 55.2 + - - +
402A HIS 3.1 19.4 + - - +
405A GLY* 4.5 7.0 - - - -
409A LEU* 4.7 10.5 - - + -
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Residues in contact with SER 401 (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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364A ALA* 2.8 42.1 + - - +
365A ILE* 3.9 0.9 + - - -
368A ASN* 3.0 10.7 + - - +
397A VAL* 3.0 18.8 + - - +
398A ALA* 3.9 13.6 - - - -
399A ILE 3.5 1.6 - - - -
400A ALA* 1.3 76.3 - - - +
402A HIS* 1.3 73.4 + - - +
22C G 4.4 10.0 + - - -
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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