Contacts of the helix formed by residues 58 - 71 (chain D) in PDB entry 2GOO
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 58 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASN 3.9 0.6 + - - +
57D SER* 1.3 77.9 - - - +
59D ASN* 1.3 64.8 + - - +
60D HIS* 3.2 11.0 + - - +
61D ALA* 3.1 22.7 + - - +
62D ILE* 3.2 23.5 + - - +
113D CYS 4.1 3.0 + - - -
114D ARG* 3.8 30.3 + - - +
81E GLU* 5.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D SER 4.1 0.4 + - - -
58D THR* 1.3 72.9 - - - +
60D HIS* 1.3 57.1 + - - +
62D ILE* 3.3 7.5 + - - +
63D VAL* 3.0 33.0 + - + +
81E GLU* 3.4 29.1 + - - +
82E GLY* 3.1 33.6 + - - +
85E PHE* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D THR* 3.1 9.8 + - - +
59D ASN* 1.3 75.8 - - - +
61D ALA* 1.3 62.7 + - - +
63D VAL* 3.2 10.6 + - + +
64D GLN* 2.8 56.6 + - + +
114D ARG* 4.7 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 3.9 9.4 - - + -
58D THR* 3.1 22.4 + - - +
60D HIS* 1.3 75.8 + - - +
62D ILE* 1.3 53.9 + - - +
64D GLN* 3.9 4.5 - - - +
65D THR* 2.8 38.3 + - - -
77D ALA* 3.9 16.3 - - + +
113D CYS 3.7 22.0 - - - +
114D ARG* 3.7 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D PHE* 6.4 0.2 - - + -
51D LEU* 4.0 16.4 - - + +
57D SER* 4.2 9.9 - - - +
58D THR 3.2 17.8 + - - +
59D ASN* 3.5 7.2 - - - +
60D HIS 3.2 0.2 - - - -
61D ALA* 1.3 74.8 - - - +
63D VAL* 1.3 63.5 + - - +
65D THR* 3.5 4.2 + - - -
66D LEU* 3.1 24.1 + - + +
81E GLU 3.7 9.4 - - - +
82E GLY* 3.6 26.0 - - - +
85E PHE* 3.9 26.2 - - + -
86E GLN* 3.5 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ASN* 3.0 20.0 + - + +
60D HIS* 3.2 12.8 + - + +
62D ILE* 1.3 74.2 - - - +
64D GLN* 1.3 58.8 + - - +
66D LEU* 3.1 9.9 + - + +
67D VAL* 2.8 41.1 + - + +
85E PHE* 4.1 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D HIS* 2.8 47.0 + - + +
61D ALA* 3.9 5.8 - - - +
63D VAL* 1.3 73.9 - - - +
65D THR* 1.3 52.8 + - - +
67D VAL* 3.8 6.3 - - - +
68D ASN* 2.8 34.1 + - - +
74D ILE* 4.0 13.0 - - + +
75D PRO* 2.8 37.6 + - - +
76D LYS 3.4 17.3 + - - -
77D ALA* 4.3 7.7 - - - +
114D ARG* 5.2 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D CYS 4.3 8.3 + - - +
48D PRO 3.8 23.3 - - - +
49D PHE* 3.9 26.2 - - + +
51D LEU* 3.5 20.6 - - + +
61D ALA 2.8 22.1 + - - -
62D ILE* 3.6 6.3 - - - -
64D GLN* 1.3 76.4 - - - +
66D LEU* 1.3 60.5 + - - +
68D ASN* 3.5 8.6 + - - +
69D SER* 3.1 21.7 + - - -
76D LYS* 5.5 3.1 - - + +
77D ALA* 4.1 13.6 + - - +
86E GLN* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D PHE* 3.7 21.3 - - + -
62D ILE* 3.1 20.5 + - + +
63D VAL* 3.1 11.7 + - + +
65D THR* 1.3 73.3 - - - +
67D VAL* 1.3 64.6 + - + +
69D SER* 2.8 20.9 + - - -
70D VAL* 3.3 12.5 + - - +
85E PHE* 3.7 38.1 - - + +
86E GLN 4.6 0.4 - - - +
89E ASP* 3.4 28.5 - - - +
90E SER* 3.8 17.0 - - - +
97E ARG* 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D VAL* 2.8 36.7 + - + +
64D GLN* 3.8 7.0 - - - +
66D LEU* 1.3 68.5 - - + +
68D ASN* 1.3 54.6 + - - +
70D VAL* 2.9 10.8 + - + +
71D ASN* 2.7 36.4 + - + +
74D ILE* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLN 2.8 21.3 + - - +
65D THR 3.7 6.3 - - - +
67D VAL* 1.3 73.2 - - - +
69D SER* 1.3 65.5 + - - +
71D ASN 3.3 22.4 - - - -
72D SER* 3.4 20.6 + - - +
74D ILE* 2.6 27.0 + - - +
75D PRO* 3.8 7.5 - - - +
76D LYS* 3.5 45.0 + - + +
94E GLN* 3.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D PHE* 5.6 1.6 - - - -
65D THR 3.1 13.5 + - - -
66D LEU* 2.8 18.6 + - - +
67D VAL 3.2 0.2 - - - -
68D ASN* 1.3 79.5 + - - +
70D VAL* 1.3 53.7 + - - +
90E SER* 5.0 0.3 - - - -
93E ALA* 3.7 7.2 - - - +
94E GLN* 2.8 40.2 + - - +
95E LEU 4.8 0.2 + - - -
97E ARG* 3.0 41.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU 3.6 13.5 - - - +
67D VAL* 2.9 9.9 + - + +
69D SER* 1.3 79.5 - - - +
71D ASN* 1.3 61.3 + - + +
90E SER* 3.2 29.6 - - - +
92E LYS* 3.8 34.4 - - + +
93E ALA* 4.0 0.9 - - - +
94E GLN* 3.4 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 2.7 16.8 + - + +
68D ASN* 3.3 15.8 - - - +
70D VAL* 1.3 79.2 - - + +
72D SER* 1.3 59.6 + - - +
73D LYS* 2.9 44.5 + - - +
74D ILE* 3.1 31.1 + - + +
94E GLN* 4.9 0.7 - - - +
----------------------------------------------------------
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