Contacts of the helix formed by residues 121 - 131 (chain A) in PDB entry 1T43
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 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 3.3 22.2 + - - -
120A THR* 1.3 77.9 - - - +
122A ALA* 1.3 53.5 + - - +
123A ILE 3.5 1.8 - - - -
124A ALA* 4.1 2.9 - - - -
125A LEU* 2.5 61.6 + - - +
138A ALA* 5.4 0.7 - - - -
149A ALA* 4.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.0 34.8 - - + -
82A LEU* 3.7 16.6 - - + -
91A PRO* 4.2 15.0 - - + -
118A THR 4.1 1.6 + - - -
120A THR* 3.0 14.3 + - - +
121A GLY* 1.3 78.0 - - - +
123A ILE* 1.3 60.7 + - + +
125A LEU* 3.6 1.2 - - - +
126A ALA 3.1 15.2 + - - -
300A SAH 4.5 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 4.2 5.8 - - + -
95A THR* 3.5 16.8 - - + -
98A LEU* 3.2 33.4 - - + +
99A VAL* 3.8 26.0 - - + -
115A ASP* 2.9 20.3 + - - +
118A THR 5.3 1.0 + - - -
122A ALA* 1.3 80.4 - - + +
124A ALA* 1.3 66.2 + - - +
125A LEU 3.0 1.6 - - - -
126A ALA* 3.2 1.1 + - - +
127A LEU* 2.8 49.8 + - + +
181A VAL* 4.3 13.9 - - + -
182A SER* 5.3 0.4 - - - -
183A ASN* 4.3 4.9 - - + +
300A SAH 4.0 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP* 2.8 36.1 + - + +
118A THR* 3.9 12.3 - - - +
121A GLY* 3.5 4.0 + - - +
123A ILE* 1.3 73.6 - - - +
125A LEU* 1.3 63.9 + - + +
127A LEU* 3.2 5.1 - - - +
128A ALA* 2.8 27.5 + - - +
136A ILE* 3.4 27.3 - - + +
137A ILE 5.0 0.2 - - - +
138A ALA* 4.4 8.7 - - + -
161A ILE* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 5.0 5.3 - - + +
82A LEU* 4.6 11.9 - - + -
120A THR 3.8 7.6 - - - +
121A GLY* 2.5 49.7 + - - +
122A ALA* 3.6 4.0 - - - +
123A ILE 3.0 0.2 - - - -
124A ALA* 1.3 73.9 - - + +
126A ALA* 1.3 58.0 + - - +
127A LEU 2.9 9.8 + - - -
128A ALA* 3.2 8.7 + - - +
129A SER* 3.5 12.8 + - - -
149A ALA* 5.1 1.3 - - + +
152A ASN* 4.3 16.4 - - + -
153A ALA* 4.5 8.1 - - + +
156A LEU* 4.7 11.4 - - + +
158A ILE* 3.1 35.3 - - + +
161A ILE* 3.3 20.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
77A PHE* 3.7 18.8 - - + -
79A SER* 4.4 13.2 - - - +
80A LEU* 4.5 8.7 - - + +
99A VAL* 4.3 17.7 - - + +
103A LEU* 5.2 1.9 - - - +
122A ALA 3.1 15.7 + - - +
123A ILE 4.0 2.5 - - - +
125A LEU* 1.3 75.7 - - - +
127A LEU* 1.3 59.7 + - - +
129A SER* 3.4 16.1 + - - -
130A GLU* 3.8 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 4.4 15.3 - - + -
102A ALA* 4.1 16.6 - - + -
103A LEU* 4.5 7.3 - - + +
106A LEU* 3.7 28.7 - - + +
113A ILE* 4.4 16.8 - - + -
115A ASP* 4.8 2.9 - - + +
123A ILE* 2.8 40.6 + - + +
124A ALA* 3.2 8.7 - - - +
126A ALA* 1.3 76.6 - - - +
128A ALA* 1.3 65.8 + - - +
129A SER 3.3 0.4 + - - -
130A GLU* 3.5 4.0 + - - +
131A ARG* 3.2 23.1 + - - +
136A ILE* 4.4 9.0 - - + -
181A VAL* 4.3 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA 2.8 14.6 + - - +
125A LEU 3.2 3.3 + - - +
127A LEU* 1.3 71.4 - - - +
129A SER* 1.3 60.4 + - - +
131A ARG 2.9 26.5 - - - +
132A PRO* 3.1 8.7 - - + +
134A CYS 5.4 0.7 - - - +
136A ILE* 2.8 38.1 - - + -
158A ILE* 4.7 10.3 - - + -
159A LYS 4.6 5.1 - - - +
161A ILE* 3.6 14.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
80A LEU* 4.6 12.5 - - - +
125A LEU 3.5 10.0 + - - -
126A ALA* 3.4 17.0 + - - -
128A ALA* 1.3 75.6 - - - +
130A GLU* 1.3 80.3 + - - +
131A ARG 3.3 0.2 + - - -
132A PRO* 3.5 13.5 - - - +
156A LEU* 5.5 0.9 - - - -
158A ILE* 4.4 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 5.4 5.2 + - - -
103A LEU* 4.4 28.9 - - + +
126A ALA* 3.8 17.7 - - - +
127A LEU 3.5 4.2 + - - +
128A ALA 3.3 0.2 - - - -
129A SER* 1.3 91.4 + - - +
131A ARG* 1.3 66.2 + - + +
132A PRO* 3.3 8.2 - - - +
133A ASP* 4.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.3 11.3 - - + +
106A LEU* 3.1 43.5 - - + +
107A PRO* 3.4 32.8 - - - +
110A PRO* 3.8 19.1 - - - +
127A LEU 3.2 13.4 + - - +
128A ALA* 2.9 13.2 + - - +
130A GLU* 1.3 86.0 + - + +
132A PRO* 1.3 56.0 - - - +
133A ASP* 3.1 26.9 + - - -
134A CYS* 3.0 40.2 - - - +
----------------------------------------------------------
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