Contacts of the helix formed by residues 561 - 569 (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 561 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A CYS* 4.0 3.8 - - - -
560A LEU* 1.3 76.9 - - - +
562A PRO* 1.3 80.2 - - - +
563A ALA* 3.0 17.6 + - + +
564A GLN* 3.2 38.1 + - + +
565A VAL* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A HIS 4.4 11.7 - - - +
525A GLY* 4.9 6.5 - - - +
526A LEU* 4.3 20.2 - - + -
530A GLN* 5.4 1.8 - - - +
551A LEU* 4.2 17.7 - - + -
555A CYS* 4.0 11.7 - - - -
560A LEU 4.6 0.2 - - - +
561A THR* 1.3 90.9 - - - +
563A ALA* 1.3 51.6 + - - +
565A VAL* 3.3 1.6 + - - +
566A VAL* 2.7 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLN* 4.1 10.7 - - - +
561A THR* 3.0 13.0 + - + +
562A PRO* 1.3 76.8 - - - +
564A GLN* 1.3 67.5 + - + +
566A VAL* 2.8 27.0 + - - +
567A ALA* 2.9 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A GLY 5.4 0.3 - - - +
560A LEU* 3.5 22.7 - - + +
561A THR* 3.2 28.5 + - + +
563A ALA* 1.3 79.8 - - + +
565A VAL* 1.3 57.6 + - - +
567A ALA* 3.5 7.9 + - - +
568A ILE* 2.9 32.5 + - - +
597A ASP* 3.4 31.9 + - - +
600A VAL* 3.5 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A VAL* 4.4 8.5 - - + -
550A LEU 5.1 0.2 - - - +
551A LEU* 3.5 32.8 - - + +
554A LEU* 4.1 29.6 - - + -
555A CYS* 5.0 0.9 - - - -
560A LEU* 4.1 21.1 - - + -
561A THR 3.0 16.2 + - - +
562A PRO 3.8 1.8 - - - +
563A ALA 2.8 2.6 + - - -
564A GLN* 1.3 71.8 - - - +
566A VAL* 1.3 63.0 + - + +
567A ALA 2.8 10.4 + - - -
568A ILE* 2.9 15.9 + - + +
569A ALA* 2.9 12.6 + - - +
578A LEU* 4.2 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A LEU* 3.7 35.7 - - + -
530A GLN* 3.4 39.2 - - + +
533A ALA* 5.5 0.5 - - - +
534A ILE* 3.8 16.9 - - + +
547A VAL* 4.8 2.9 - - + -
551A LEU* 5.4 1.6 - - + -
562A PRO* 2.7 28.2 + - + +
563A ALA* 2.8 9.5 + - - +
565A VAL* 1.3 76.9 - - + +
567A ALA* 1.3 56.9 + - + +
569A ALA* 3.9 10.1 - - - +
570A SER* 3.1 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ALA 2.9 12.5 + - - +
564A GLN* 4.0 7.9 - - - +
565A VAL 2.8 1.2 - - - -
566A VAL* 1.3 81.5 - - + +
568A ILE* 1.3 61.2 + - - +
569A ALA 3.2 0.7 - - - -
570A SER* 4.3 5.2 - - - +
571A HIS* 3.0 26.7 + - - +
600A VAL* 5.9 0.9 - - + -
604A SER* 3.1 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LEU* 4.7 7.0 - - + -
564A GLN 2.9 20.6 + - - +
565A VAL* 2.9 7.4 + - - +
567A ALA* 1.3 79.3 - - - +
569A ALA* 1.3 59.3 + - - +
570A SER 3.7 0.2 - - - -
571A HIS* 4.0 9.5 + - - +
574A GLY* 4.4 5.0 - - - +
577A ALA* 3.9 21.7 - - + +
578A LEU* 4.0 26.0 - - + +
581A VAL* 4.1 18.6 - - + -
600A VAL* 4.1 17.0 - - + -
603A ALA* 3.1 43.2 - - + +
604A SER* 3.4 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ILE* 3.5 38.4 - - + +
537A HIS* 4.8 0.3 + - - +
543A ALA* 3.8 19.4 - - + +
547A VAL* 3.5 15.9 - - + -
565A VAL 2.9 15.5 + - - +
566A VAL 4.0 1.6 - - - +
567A ALA 3.2 0.2 - - - -
568A ILE* 1.3 76.0 - - - +
570A SER* 1.3 57.3 + - - +
571A HIS 3.1 13.2 + - - +
574A GLY* 3.9 11.4 - - - -
578A LEU* 4.7 5.6 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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