Contacts of the helix formed by residues 527 - 536 (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 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A GLY 5.5 1.8 - - - +
526A LEU* 1.3 77.8 - - - +
528A PRO* 1.3 61.1 - - + +
529A ASP* 2.7 22.0 + - - +
530A GLN* 3.0 31.4 + - - +
531A VAL* 2.9 24.0 + - - +
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Residues in contact with PRO 528 (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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491A HIS* 4.6 10.1 - - + +
493A LEU* 4.3 17.7 - - + +
497A GLN* 3.9 0.7 + - - -
517A LEU* 4.3 17.0 - - + -
521A CYS* 3.8 26.7 - - + -
522A GLN* 5.4 0.4 - - - +
526A LEU 4.2 0.4 - - - +
527A THR* 1.3 85.0 - - + +
529A ASP* 1.3 61.6 + - - +
531A VAL* 3.8 11.6 - - + +
532A VAL* 2.8 31.1 + - - +
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Residues in contact with ASP 529 (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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493A LEU* 5.2 0.2 - - - +
497A GLN* 2.6 33.4 + - - -
527A THR* 2.7 14.3 + - - +
528A PRO* 1.3 77.5 - - - +
530A GLN* 1.3 57.5 + - - +
531A VAL 2.9 1.1 - - - -
532A VAL* 3.9 2.7 - - - +
533A ALA* 2.7 31.1 + - - +
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Residues in contact with GLN 530 (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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525A GLY 3.8 3.9 + - - +
526A LEU* 3.2 30.0 - - + +
527A THR* 3.0 27.4 + - - +
529A ASP* 1.3 76.5 - - - +
531A VAL* 1.3 61.8 + - - +
533A ALA* 3.4 8.8 - - - +
534A ILE* 3.1 27.9 + - - +
562A PRO* 4.9 1.4 - - - +
563A ALA* 4.1 17.0 - - - +
566A VAL* 3.4 37.1 - - + +
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Residues in contact with VAL 531 (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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513A VAL* 4.2 15.3 - - + -
516A LEU 5.9 0.4 - - - -
517A LEU* 4.3 17.3 - - + -
520A LEU* 4.8 6.3 - - + -
521A CYS* 4.3 12.1 - - + +
526A LEU* 3.8 29.2 - - + -
527A THR 2.9 22.9 + - - +
528A PRO* 4.2 8.3 - - + -
530A GLN* 1.3 77.3 - - - +
532A VAL* 1.3 67.9 + - + +
534A ILE* 2.9 9.3 + - - +
535A ALA* 2.9 20.3 + - - +
544A LEU* 3.7 22.6 - - + +
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Residues in contact with VAL 532 (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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493A LEU* 4.2 14.8 - - + -
497A GLN* 3.5 37.9 - - + +
500A ALA* 5.4 2.7 - - + -
501A ILE* 3.5 32.1 - - + +
513A VAL* 5.5 2.2 - - + -
517A LEU* 6.2 1.1 - - + -
528A PRO 2.8 25.4 + - - +
529A ASP* 3.9 2.9 - - - +
531A VAL* 1.3 76.2 - - + +
533A ALA* 1.3 67.7 + - - +
535A ALA* 2.7 12.2 + - - +
536A SER* 2.6 30.9 + - - +
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Residues in contact with ALA 533 (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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529A ASP 2.7 22.9 + - - +
530A GLN* 3.4 12.6 - - - +
532A VAL* 1.3 75.3 - - - +
534A ILE* 1.3 57.6 + - - +
536A SER* 3.5 5.0 + - - -
537A HIS* 2.9 30.1 + - + -
566A VAL 5.5 0.7 - - - +
570A SER* 3.3 13.2 - - - +
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Residues in contact with ILE 534 (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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526A LEU* 4.8 4.7 - - + -
530A GLN 3.1 13.5 + - - +
531A VAL* 2.9 8.9 + - - +
532A VAL 2.9 0.8 + - - -
533A ALA* 1.3 74.3 - - - +
535A ALA* 1.3 59.8 + - - +
536A SER 3.2 4.0 + - - -
537A HIS* 3.7 12.3 + - - +
540A GLY* 4.6 7.3 + - - +
543A ALA* 3.8 13.4 - - + +
544A LEU* 3.8 36.3 - - + +
547A VAL* 3.6 22.0 - - + -
566A VAL* 3.8 23.3 - - + +
569A ALA* 3.5 27.7 - - + +
570A SER* 3.4 16.8 - - - +
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Residues in contact with ALA 535 (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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501A ILE* 3.3 29.1 - - + +
505A GLY* 3.7 2.5 - - - -
509A ALA* 3.5 15.2 - - + +
513A VAL* 3.5 32.5 - - + -
531A VAL 2.9 8.1 + - - +
532A VAL 2.7 11.5 + - - +
534A ILE* 1.3 71.5 - - - +
536A SER* 1.3 56.3 + - - -
537A HIS 3.6 5.0 + - - -
540A GLY* 4.7 6.5 - - - -
544A LEU* 3.5 13.7 - - + -
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Residues in contact with SER 536 (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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500A ALA* 4.0 16.1 - - - +
501A ILE* 3.7 5.3 + - - +
504A ASN* 3.0 25.1 + - - +
532A VAL* 2.6 40.8 + - - +
533A ALA* 3.5 6.0 + - - -
534A ILE 3.2 3.0 - - - -
535A ALA* 1.3 75.5 - - - +
537A HIS* 1.3 80.7 + - - +
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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