Contacts of the helix formed by residues 94 - 104 (chain A) in PDB entry 6B0Z
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 94 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 3.4 15.0 + - - +
92A TRP 3.7 1.8 + - - -
93A LYS* 1.3 76.6 - - - +
95A PRO* 1.3 70.7 - - - +
96A ASN* 3.3 14.7 + - - +
97A GLY* 3.2 10.6 + - - -
98A THR* 3.1 19.6 + - - -
503A FLC 2.5 40.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.4 15.0 - - + -
49A ARG* 3.2 40.6 - - - +
57A THR* 3.7 23.3 - - + +
72A LYS* 4.4 2.9 - - - -
75A THR* 3.6 23.6 - - - +
76A ILE 4.3 1.3 - - - +
77A THR* 4.0 9.0 - - - +
93A LYS 3.2 7.8 - - - +
94A SER* 1.3 84.2 - - - +
96A ASN* 1.3 58.7 + - - +
98A THR* 3.2 3.0 + - - -
99A ILE* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 3.0 28.1 + - - +
75A THR* 3.8 7.5 + - - -
77A THR* 4.4 1.4 + - - -
94A SER* 3.1 13.2 + - - +
95A PRO* 1.3 76.3 - - - +
97A GLY* 1.3 60.4 + - - +
99A ILE* 3.3 7.2 + - - +
100A ARG* 3.0 56.5 + - - +
304A GLU* 5.2 0.8 - - - +
306A GLU* 3.5 16.3 - - - +
501A NDP 3.3 31.0 + - - -
503A FLC 3.5 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 3.6 13.2 + - - -
94A SER* 3.2 16.0 + - - -
96A ASN* 1.3 78.3 - - - +
98A THR* 1.3 61.0 + - - +
100A ARG* 3.8 15.4 - - - +
101A ASN* 3.1 26.3 + - - +
503A FLC 4.9 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 4.1 12.2 + - - +
57A THR* 3.9 21.0 - - + +
58A LYS* 4.2 17.7 - - + -
93A LYS* 3.4 32.0 - - - +
94A SER 3.1 9.5 + - - -
95A PRO 3.5 8.1 - - - -
97A GLY* 1.3 76.7 - - - +
99A ILE* 1.3 62.1 + - - +
101A ASN* 3.6 2.6 - - - +
102A ILE* 3.1 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 3.8 23.1 - - - -
44A LEU* 4.3 8.7 - - + -
57A THR* 4.4 11.7 - - + +
60A ALA* 5.3 0.7 - - + -
61A ALA* 4.1 19.5 - - + -
64A ILE* 4.3 5.6 - - + -
72A LYS* 3.9 15.9 - - + -
95A PRO 2.9 18.8 + - - +
96A ASN* 3.8 5.4 - - - +
98A THR* 1.3 77.7 - - - +
100A ARG* 1.3 59.6 + - + +
102A ILE* 3.1 3.3 + - - +
103A LEU* 2.8 51.8 + - + +
295A LEU* 4.8 0.2 - - + -
304A GLU* 3.8 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASN* 3.0 27.8 + - - +
97A GLY* 3.8 16.1 - - - +
99A ILE* 1.3 75.0 - - + +
101A ASN* 1.3 59.5 + - - +
103A LEU 4.3 0.2 - - - +
104A GLY* 2.6 34.9 + - - +
105A GLY 5.9 0.7 - - - +
107A VAL* 3.9 28.0 - - - +
295A LEU* 4.3 26.7 - - + -
304A GLU* 5.2 3.1 - - - +
306A GLU* 5.3 6.1 + - - -
503A FLC 2.6 44.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 4.4 12.4 - - - +
97A GLY 3.1 20.5 + - - +
98A THR* 3.6 4.6 + - - +
100A ARG* 1.3 77.1 - - - +
102A ILE* 1.3 73.2 + - - +
104A GLY* 4.1 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS* 4.2 19.3 - - + +
61A ALA* 3.6 31.4 - - + -
62A GLU* 3.6 28.5 - - - +
65A LYS* 4.3 21.6 + - + +
98A THR* 3.1 26.2 + - + +
99A ILE 3.1 7.8 + - - +
101A ASN* 1.3 89.0 - - - +
103A LEU* 1.3 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 3.4 26.0 - - + +
64A ILE* 3.6 26.2 - - + -
65A LYS* 3.8 29.6 - - + +
99A ILE* 2.8 37.8 + - + +
102A ILE* 1.3 80.8 - - - +
104A GLY* 1.3 70.8 + - - +
295A LEU* 3.9 16.2 - - + -
297A CYS* 3.8 16.8 - - - +
298A PRO* 5.2 1.7 - - - +
302A THR* 4.7 8.3 - - + -
304A GLU* 4.5 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 2.6 23.1 + - - -
101A ASN 4.1 2.7 + - - -
102A ILE 3.5 1.6 - - - -
103A LEU* 1.3 82.2 - - - +
105A GLY* 1.3 60.5 + - - -
295A LEU* 3.7 12.6 - - - +
297A CYS* 3.6 12.0 - - - -
298A PRO* 4.7 1.8 - - - -
----------------------------------------------------------
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