Contacts of the helix formed by residues 125 - 135 (chain A) in PDB entry 4CCG
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 MET 125 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS 3.7 8.5 - - - +
77A PRO 3.1 4.8 + - - +
79A ILE 3.4 22.0 - - - +
80A ASP* 3.4 26.0 - - - -
81A SER* 3.4 26.0 - - - +
123A PRO* 4.6 0.2 - - - -
124A LEU* 1.3 82.0 - - - +
126A ALA* 1.3 59.8 + - - +
127A ASP* 3.2 19.7 - - - +
128A ILE* 3.3 25.5 + - + +
129A SER* 2.8 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 4.7 8.2 - - + +
124A LEU 3.8 3.8 + - - -
125A MET* 1.3 72.2 - - - +
127A ASP* 1.3 58.3 + - - +
129A SER* 3.6 7.7 - - - -
130A SER* 3.0 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET* 3.5 27.1 - - - +
126A ALA* 1.3 72.6 + - - +
128A ILE* 1.3 88.5 + - - +
130A SER* 3.2 7.2 + - - -
131A GLU* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE 5.5 0.4 - - - +
75A TYR* 3.7 44.6 - - + +
76A HIS 3.7 19.1 - - - +
77A PRO* 3.6 20.2 - - + -
79A ILE 5.3 0.2 - - - +
125A MET* 3.3 27.8 + - + +
127A ASP* 1.3 92.4 + - - +
129A SER* 1.3 57.6 + - - +
131A GLU* 3.3 6.7 + - - +
132A PHE* 2.9 27.9 + - - +
139A PHE* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 3.9 18.6 - - - +
120A PRO* 4.4 15.9 + - - +
123A PRO* 3.5 28.0 - - - +
125A MET 2.8 18.4 + - - -
126A ALA* 3.6 5.8 - - - -
127A ASP 3.2 0.2 - - - -
128A ILE* 1.3 78.0 - - - +
130A SER* 1.3 62.1 + - - +
132A PHE* 3.4 5.2 + - - +
133A LYS* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 3.0 17.5 + - - -
127A ASP* 3.7 5.6 - - - -
129A SER* 1.3 73.3 - - - +
131A GLU* 1.3 62.2 + - - +
133A LYS* 3.2 2.0 + - - -
134A TYR* 3.0 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 2.4 35.6 + - - -
127A ASP 3.0 13.8 + - - +
128A ILE* 3.6 7.1 - - - +
130A SER* 1.3 75.5 - - - +
132A PHE* 1.3 57.2 + - - +
134A TYR* 5.4 0.2 - - - -
135A ASN* 2.8 46.7 + - + +
138A ALA* 3.6 12.8 - - + +
139A PHE* 3.5 20.3 - - - +
142A ASN* 2.6 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 4.0 13.9 - - + -
118A PRO* 3.5 46.7 - - + -
120A PRO* 5.7 11.7 - - + -
128A ILE 2.9 16.8 + - - +
129A SER* 3.6 6.5 - - - +
130A SER 3.3 0.2 - - - -
131A GLU* 1.3 76.0 - - - +
133A LYS* 1.3 63.7 + - + +
136A LYS* 3.0 60.3 + - + +
139A PHE* 3.6 43.0 - + + +
140A LEU* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 6.0 8.7 - - + -
129A SER 3.1 15.2 + - - +
130A SER* 3.2 4.2 + - - +
132A PHE* 1.3 86.3 - - + +
134A TYR* 1.3 103.6 + - + +
136A LYS* 4.4 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER* 3.0 39.6 + - - +
131A GLU* 5.4 0.2 - - - -
133A LYS* 1.3 118.7 - - + +
135A ASN* 1.3 63.1 + - + +
136A LYS* 4.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU* 2.8 23.7 + - + +
133A LYS 3.7 0.4 - - - -
134A TYR* 1.3 82.6 - - + +
136A LYS* 1.3 64.5 + - - +
137A PRO* 3.5 10.6 - - - +
138A ALA* 3.2 31.4 + - + +
139A PHE 3.0 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