Contacts of the helix formed by residues 97 - 106 (chain Z) in PDB entry 3CC2
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 97 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18760 C 5.9 3.4 - - - -
72A GLU* 2.5 31.2 + - - +
158A VAL* 4.7 2.1 - - - +
162A GLY* 3.8 22.4 - - - +
163A GLY* 5.7 0.2 - - - -
91Z GLY* 3.5 27.4 - - - -
94Z LYS* 4.8 7.4 - - + +
96Z GLU* 1.3 74.9 - - - +
98Z PRO* 1.3 72.8 - - + +
99Z GLY* 3.6 4.1 + - - -
100Z GLY 3.0 12.8 + - - -
101Z LYS* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 98 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Z LYS* 5.0 13.0 - - - -
96Z GLU 4.7 0.7 - - - +
97Z THR* 1.3 89.7 - - + +
99Z GLY* 1.3 60.8 - - - +
101Z LYS* 3.5 12.6 + - + +
102Z THR* 3.2 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY 6.1 1.3 - - - -
125A ASN* 5.7 2.2 - - - -
158A VAL* 3.9 18.8 - - - +
97Z THR* 3.1 5.2 + - - -
98Z PRO* 1.3 81.2 - - - +
100Z GLY* 1.3 60.8 + - - +
102Z THR* 3.2 20.5 + - - +
103Z VAL* 3.5 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 3.7 25.1 - - - -
158A VAL* 3.9 10.8 - - - +
96Z GLU* 6.4 0.2 - - - -
97Z THR* 3.0 15.2 + - - -
99Z GLY* 1.3 77.3 - - - +
101Z LYS* 1.3 60.3 + - - +
102Z THR 3.3 0.5 + - - -
103Z VAL* 3.4 19.5 + - - +
104Z ARG* 4.0 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Z GLU* 3.4 46.0 - - + +
97Z THR 3.0 19.8 + - - +
98Z PRO* 3.9 9.6 - - + +
99Z GLY 3.3 0.2 - - - -
100Z GLY* 1.3 76.4 - - - +
102Z THR* 1.3 60.6 + - - +
103Z VAL 3.4 0.2 - - - -
104Z ARG* 4.0 27.7 + - - +
105Z ARG* 4.2 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 4.4 16.6 - - + -
98Z PRO 3.2 12.8 + - - -
99Z GLY* 3.2 13.7 + - - +
100Z GLY 3.1 0.6 - - - -
101Z LYS* 1.3 78.7 - - - +
103Z VAL* 1.3 68.2 + - - +
105Z ARG* 3.2 37.7 + - - +
106Z SER* 3.7 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 3.7 28.5 - - + -
103A VAL* 5.6 2.1 - - + +
104A PRO* 4.4 20.5 - - + +
156A ILE* 4.6 6.7 - - + -
157A GLY* 3.9 17.7 - - - +
158A VAL* 3.9 29.4 - - + +
99Z GLY 3.5 14.4 - - - +
100Z GLY* 3.5 13.9 - - - +
102Z THR* 1.3 79.9 - - - +
104Z ARG* 1.3 65.3 + - + +
105Z ARG 3.2 0.2 + - - -
106Z SER* 3.7 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 5.6 6.3 - - + -
64Z PRO* 5.8 7.1 - - - +
96Z GLU* 3.0 40.1 + - - +
100Z GLY 4.2 9.8 + - - +
101Z LYS* 4.0 23.0 - - - +
102Z THR 3.3 0.2 - - - -
103Z VAL* 1.3 78.6 - - + +
105Z ARG* 1.3 68.2 - - + +
106Z SER 4.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Z LYS 4.3 7.3 + - - +
102Z THR* 3.2 30.6 + - - +
104Z ARG* 1.3 81.9 - - + +
106Z SER* 1.3 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PRO* 6.2 0.2 - - - -
101A GLU 5.8 0.2 - - - -
102A GLY 3.5 26.4 + - - -
103A VAL* 4.4 19.3 - - - -
104A PRO* 4.0 12.1 - - - +
102Z THR* 3.7 14.7 + - - +
103Z VAL 3.7 10.5 + - - -
104Z ARG 4.0 2.4 - - - +
105Z ARG* 1.3 85.8 - - - +
----------------------------------------------------------
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