Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 1UPD
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 SER 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL 3.0 28.9 - - - -
68A VAL 3.7 5.2 - - - -
70A ALA 2.6 28.7 + - - -
74A LEU* 4.1 12.7 - - - +
76A HIS 3.5 3.8 + - - -
77A THR* 1.3 79.1 - - - +
79A CYS* 1.3 65.2 + - - +
80A LEU 3.6 0.9 + - - -
81A ALA* 3.0 17.3 + - - +
82A CYS 3.1 17.7 + - - -
1109A HEC 4.5 1.8 - - - -
1110A HEC 3.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL 4.1 0.8 + - - -
68A VAL* 3.3 31.3 + - - +
78A SER* 1.3 74.3 - - - +
80A LEU* 1.3 59.1 + - + +
82A CYS* 3.4 0.9 + - - +
83A HIS* 3.0 35.7 + - - -
1109A HEC 5.9 2.0 - - - -
1110A HEC 1.8 77.1 - - + +
1111A HEC 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL 3.1 14.3 + - - +
69A HIS* 3.5 36.3 - - + +
70A ALA 4.2 1.8 - - - +
71A ARG* 5.1 4.9 - - + +
78A SER 3.3 0.2 - - - -
79A CYS* 1.3 78.3 - - + +
81A ALA* 1.3 59.8 + - - +
83A HIS* 4.0 2.2 - - - +
84A SER* 2.8 38.8 + - - +
97A LEU 4.5 0.7 - - - +
98A THR* 4.1 39.0 - - + +
1111A HEC 3.8 53.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 3.9 6.4 + - - +
71A ARG* 4.7 13.7 - - - +
72A GLY 5.2 3.6 - - - +
77A THR* 4.2 7.4 - - + -
78A SER* 3.0 29.7 + - - +
80A LEU* 1.3 79.4 - - - +
82A CYS* 1.3 64.2 + - - +
84A SER* 3.4 10.3 + - - -
85A LYS* 3.4 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 3.7 10.0 - - + +
78A SER 3.1 6.8 + - - +
81A ALA* 1.3 78.7 - - - +
83A HIS* 1.3 63.4 + - - +
85A LYS* 2.9 17.1 + - + +
86A VAL* 2.9 25.5 + - - +
1110A HEC 1.8 78.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A CYS 3.0 17.4 + - - +
80A LEU* 4.0 3.8 - - - +
82A CYS* 1.3 77.7 - - - +
84A SER* 1.3 56.9 + - - +
86A VAL* 3.1 5.0 + - - +
87A VAL* 2.8 35.2 + - - +
97A LEU* 2.8 45.2 + - + +
98A THR* 4.0 6.3 - - + -
105A CYS* 4.8 0.2 - - - -
1110A HEC 2.0 93.8 + + - -
1111A HEC 3.5 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 4.7 15.2 - - - +
80A LEU* 2.8 28.4 + - - +
81A ALA* 3.7 7.8 - - - -
82A CYS 3.2 0.2 - - - -
83A HIS* 1.3 77.5 - - - +
85A LYS* 1.3 60.3 + - - +
87A VAL* 3.4 13.5 - - - +
88A ALA* 3.1 22.5 + - - +
98A THR* 4.2 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 5.2 7.2 - - - -
81A ALA* 3.6 24.9 - - - +
82A CYS* 2.9 15.9 + - - +
84A SER* 1.3 75.0 - - - +
86A VAL* 1.3 66.8 + - + +
88A ALA* 3.3 18.9 + - - +
89A GLU* 3.5 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A CYS* 2.9 31.2 + - - +
83A HIS* 3.6 9.0 - - - +
85A LYS* 1.3 75.1 - - + +
87A VAL* 1.3 59.4 + - - +
89A GLU* 3.0 13.0 + - - +
90A LYS* 2.8 30.4 + - + +
93A LEU* 4.6 5.6 - - + -
97A LEU* 3.7 22.7 - - + -
1110A HEC 3.9 44.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS 2.8 28.2 + - - +
84A SER* 3.4 16.2 - - - +
85A LYS 3.3 0.2 - - - -
86A VAL* 1.3 68.6 - - - +
88A ALA* 1.3 66.4 + - - +
90A LYS 3.7 7.4 - - - +
91A PRO* 3.1 26.0 - - - +
93A LEU* 3.7 26.0 - - + +
94A LYS* 3.9 24.0 - - + +
97A LEU* 3.8 22.4 - - + -
98A THR* 4.0 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER 3.1 14.2 + - - +
85A LYS* 3.5 13.5 - - - +
86A VAL 3.2 0.4 - - - -
87A VAL* 1.3 79.0 - - - +
89A GLU* 1.3 64.0 + - + +
91A PRO* 3.9 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 3.9 14.3 - - - +
86A VAL* 3.0 10.6 + - - +
88A ALA* 1.3 79.9 - - + +
90A LYS* 1.3 66.1 + - + +
91A PRO* 3.4 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 2.8 18.5 + - + +
87A VAL* 3.3 8.7 - - - +
89A GLU* 1.3 86.5 - - + +
91A PRO* 1.3 60.1 - - - +
92A GLU* 3.1 26.5 - - - +
93A LEU* 2.9 39.1 + - + +
1110A HEC 2.8 32.5 + - - +
----------------------------------------------------------
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