Contacts of the helix formed by residues 125 - 135 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B HIS 3.5 7.6 - - - +
77B PRO 3.0 5.7 + - - +
79B ILE 3.3 21.3 - - - +
80B ASP* 3.4 26.5 - - - -
81B SER* 4.0 20.9 - - - +
123B PRO* 4.5 0.4 - - - -
124B LEU* 1.3 82.4 - - - +
126B ALA* 1.3 55.7 + - - +
127B ASP* 3.2 2.0 - - + -
128B ILE* 3.7 34.5 - - + +
129B SER* 2.7 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 4.7 7.0 - - + -
124B LEU 3.8 4.0 + - - -
125B MET* 1.3 73.1 - - - +
127B ASP* 1.3 57.3 + - - +
129B SER* 3.6 6.5 - - - -
130B SER* 3.0 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 3.2 1.0 - - + -
126B ALA* 1.3 76.6 - - - +
128B ILE* 1.3 69.0 - - + +
130B SER* 3.3 6.7 - - - -
131B GLU* 3.1 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE 5.6 0.7 - - - +
75B TYR* 3.8 43.3 - - + +
76B HIS 3.8 10.5 - - - +
77B PRO* 3.6 20.4 - - + -
79B ILE 5.1 0.9 - - - +
125B MET* 3.4 42.9 + - + -
127B ASP* 1.3 79.0 + - + +
129B SER* 1.3 57.6 + - - +
131B GLU* 3.4 6.9 + - - +
132B PHE* 3.0 27.0 + - - +
139B PHE* 3.7 21.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 4.0 14.4 - - - +
120B PRO* 3.5 23.3 + - - +
123B PRO* 3.2 28.3 - - - +
125B MET 2.7 19.4 + - - -
126B ALA* 3.6 5.4 - - - -
128B ILE* 1.3 78.0 - - - +
130B SER* 1.3 61.0 + - - +
132B PHE* 3.3 4.8 + - - +
133B LYS* 3.3 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA 3.0 19.9 + - - -
127B ASP* 3.3 6.0 - - - -
129B SER* 1.3 74.8 - - - +
131B GLU* 1.3 59.5 + - - +
133B LYS* 3.1 6.8 + - - +
134B TYR* 3.0 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 2.5 31.5 + - - -
127B ASP 3.1 13.7 - - - -
128B ILE 3.6 6.5 - - - +
129B SER 3.3 0.2 - - - -
130B SER* 1.3 76.8 - - - +
132B PHE* 1.3 58.9 + - - +
134B TYR* 5.4 0.2 - - - -
135B ASN* 2.8 46.7 + - + +
138B ALA* 3.7 12.5 - - + +
139B PHE* 3.5 24.1 - - - +
142B ASN* 2.7 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 4.1 12.8 - - + -
118B PRO* 3.7 37.7 - - + -
120B PRO* 4.1 36.6 - - + -
128B ILE 3.0 13.7 + - - +
129B SER 3.5 8.5 - - - +
130B SER 3.2 0.2 - - - -
131B GLU* 1.3 78.3 - - - +
133B LYS* 1.3 64.5 + - + +
136B LYS* 3.3 51.5 - - - +
139B PHE* 3.5 37.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 3.7 37.5 + - + +
129B SER* 3.3 17.0 + - - +
130B SER* 3.1 9.7 + - - +
132B PHE* 1.3 82.3 - - + +
134B TYR* 1.3 99.5 + - + +
135B ASN 3.6 0.2 - - - -
136B LYS* 5.0 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 3.0 36.1 + - - +
131B GLU* 5.4 0.4 - - - -
133B LYS* 1.3 116.5 + - + +
135B ASN* 1.3 63.1 + - + +
136B LYS 4.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLU* 2.8 22.5 + - + +
134B TYR* 1.3 81.6 - - + +
136B LYS* 1.3 64.4 + - - +
137B PRO* 3.4 13.4 - - - +
138B ALA* 3.1 34.2 + - + +
139B PHE 3.0 17.7 + - - -
----------------------------------------------------------
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