Contacts of the helix formed by residues 663 - 671 (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 663 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A GLY 3.5 4.5 + - - -
662A LEU* 1.3 79.0 - - - +
664A PRO* 1.3 62.2 - - - +
665A ASP* 2.6 30.8 + - + +
666A GLN* 2.5 64.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A GLY 5.5 3.6 - - - +
628A LEU* 4.6 14.8 - - + +
632A GLN* 4.2 13.2 - - - +
653A LEU* 5.7 5.2 - - + -
657A CYS* 5.0 11.2 - - - -
662A LEU 3.1 4.7 - - - +
663A THR* 1.3 83.8 - - - +
665A ASP* 1.3 69.7 + - - +
667A VAL* 2.7 22.6 + - + +
668A VAL* 2.9 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A GLN* 4.4 3.9 - - - +
663A THR* 2.6 34.8 + - + +
664A PRO* 1.3 74.9 - - - +
666A GLN* 1.3 62.2 + - + +
668A VAL* 3.0 22.8 - - - +
669A ALA* 3.2 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 3.4 29.9 - - + +
663A THR* 2.5 55.4 + - + +
665A ASP* 1.3 75.8 - - + +
667A VAL* 1.3 57.2 + - - +
669A ALA* 3.7 3.6 + - - +
670A ILE* 3.0 30.6 + - - +
698A GLN* 4.3 11.3 - - - +
699A VAL* 4.6 10.8 + - + +
702A VAL* 3.2 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A LEU* 5.9 2.5 - - + -
649A VAL* 4.2 13.9 - - + -
653A LEU* 4.2 30.7 - - + -
656A LEU* 4.2 22.2 - - + -
657A CYS* 4.7 10.3 - - - -
662A LEU* 3.8 23.1 - - + +
664A PRO* 2.7 17.4 + - + +
666A GLN* 1.3 68.4 - - - +
668A VAL* 1.3 54.8 + - - +
669A ALA 2.9 4.3 - - - -
670A ILE* 2.6 30.7 + - - +
671A ALA 3.0 10.6 + - - -
680A LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A LEU* 4.8 6.0 - - + +
632A GLN* 2.8 63.5 - - + +
635A ALA* 5.3 4.0 - - + -
636A ILE* 4.0 15.4 - - + +
664A PRO 2.9 15.0 + - - +
665A ASP* 3.0 23.8 - - - +
667A VAL* 1.3 76.6 - - - +
669A ALA* 1.3 54.6 + - + +
671A ALA* 3.8 2.8 + - - +
672A SER* 2.7 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A ASP 3.2 17.7 + - - +
666A GLN* 3.7 6.3 - - - +
667A VAL 2.9 0.8 - - - -
668A VAL* 1.3 75.4 - - + +
670A ILE* 1.3 68.7 + - + +
672A SER* 2.9 20.8 + - - -
673A ASN* 3.7 9.8 + - - -
702A VAL* 5.4 2.5 - - + -
706A SER* 4.9 13.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 4.3 16.8 - - + -
666A GLN 3.0 21.3 - - - +
667A VAL* 2.6 15.7 + - - +
669A ALA* 1.3 73.0 - - - +
671A ALA* 1.3 57.2 + - - +
672A SER 3.0 4.7 + - - -
673A ASN* 4.0 8.0 + - - +
676A GLY* 4.2 9.4 - - - -
679A ALA* 3.9 1.8 - - + +
680A LEU* 3.4 43.3 - - + +
683A VAL* 5.0 4.9 - - + -
702A VAL* 3.3 24.5 - - + +
705A ALA* 3.3 49.4 - - + +
706A SER* 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 3.1 36.1 - - + +
641A GLY* 5.0 1.0 - - - -
645A ALA* 3.8 16.7 - - + +
649A VAL* 3.6 31.9 - - + -
667A VAL 3.0 10.5 + - - +
668A VAL 4.4 0.4 - - - +
669A ALA 3.3 0.4 - - - -
670A ILE* 1.3 74.3 - - - +
672A SER* 1.3 60.1 + - - +
673A ASN 3.6 4.3 + - - +
676A GLY* 4.8 2.7 - - - -
680A LEU* 3.8 16.3 - - + +
----------------------------------------------------------
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