Contacts of the helix formed by residues 127 - 138 (chain A) in PDB entry 3KUC
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 GLY 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 4.6 1.4 + - - -
124A ARG* 3.7 8.2 + - - -
125A VAL 4.3 0.2 - - - -
126A VAL* 1.3 80.6 - - - +
128A LYS* 1.3 66.3 + - - -
129A GLU 3.3 1.8 - - - -
130A GLN* 3.0 23.1 + - - +
131A GLY* 3.1 17.8 + - - -
145A GLU* 4.3 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 3.3 13.6 - - - +
127A GLY* 1.3 72.1 - - - -
129A GLU* 1.3 65.2 + - - +
131A GLY* 3.1 4.0 + - - -
132A GLN* 2.9 43.9 + - - +
143A PHE* 3.9 10.0 - - + -
145A GLU* 3.4 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY* 3.3 0.4 - - - -
128A LYS* 1.3 79.0 - - - +
130A GLN* 1.3 53.5 + - - +
132A GLN* 3.2 19.3 + - - +
133A ASN* 2.8 58.4 + - - +
136A ARG* 4.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.7 35.6 - - + -
91A ASN* 5.5 1.2 + - - -
125A VAL 4.5 3.4 + - - +
126A VAL* 3.6 16.2 - - + +
127A GLY* 3.0 29.3 + - - +
128A LYS 3.2 0.6 - - - -
129A GLU* 1.3 77.8 - - - +
131A GLY* 1.3 60.9 + - - +
133A ASN* 3.4 12.4 + - - +
134A LEU* 3.2 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.6 23.3 - - - -
90A PHE* 3.9 13.5 - - - -
113A LEU* 3.5 8.7 - - - +
127A GLY 3.1 12.3 + - - -
128A LYS 3.6 2.2 - - - -
130A GLN* 1.3 71.3 - - - +
132A GLN* 1.3 60.9 + - - +
134A LEU 3.1 2.4 + - - -
135A ALA* 2.9 25.1 + - - +
143A PHE* 3.7 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 2.9 40.9 + - - +
129A GLU* 3.5 26.5 + - - +
131A GLY* 1.3 74.8 - - - +
133A ASN* 1.3 57.8 + - - +
135A ALA* 3.8 2.7 - - - +
136A ARG* 2.9 48.8 + - - +
143A PHE* 3.5 28.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 2.8 40.5 + - - +
130A GLN* 3.5 10.6 - - - +
132A GLN* 1.3 71.8 - - - +
134A LEU* 1.3 65.5 + - - +
136A ARG* 2.5 38.8 + - - +
137A GLN* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.8 48.0 - - + +
93A LEU* 5.0 1.8 - - + -
94A GLN* 3.8 15.7 - - + +
113A LEU* 4.2 8.3 - - + -
130A GLN 3.2 2.5 + - - +
131A GLY 3.1 8.3 + - - +
133A ASN* 1.3 78.2 - - - +
135A ALA* 1.3 62.8 + - - +
137A GLN* 3.2 37.2 + - - +
138A TRP* 3.1 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.8 12.4 - - + +
131A GLY 2.9 14.2 + - - +
132A GLN* 3.8 4.5 - - - +
134A LEU* 1.3 75.1 - - - +
136A ARG* 1.3 65.1 + - - +
138A TRP* 3.1 11.4 + - - -
141A CYS* 3.0 51.6 + - + +
142A ALA 4.2 1.6 - - - +
143A PHE* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 4.7 5.7 + - - +
132A GLN* 2.9 30.4 + - - +
133A ASN* 2.5 42.8 + - - +
135A ALA* 1.3 74.6 - - - +
137A GLN* 1.3 63.6 + - - +
139A CYS* 3.3 2.3 + - - -
140A ASN* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN* 3.2 31.5 + - - +
133A ASN 3.0 14.6 + - - +
134A LEU* 3.2 26.5 + - - +
136A ARG* 1.3 77.3 - - - +
138A TRP* 1.3 61.8 + - + +
139A CYS* 2.9 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.7 31.6 - - + -
93A LEU* 4.1 7.4 - - + -
94A GLN* 2.8 40.7 + - - -
97A ARG* 3.3 52.3 + - + +
111A MET* 4.6 2.2 - - - -
113A LEU* 3.8 35.9 - - + -
134A LEU* 3.1 38.9 + - + +
135A ALA* 3.1 10.1 + - - +
137A GLN* 1.3 80.3 - - + +
139A CYS* 1.3 70.2 + - - +
140A ASN 3.4 1.8 - - - -
141A CYS* 3.1 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