Contacts of the helix formed by residues 129 - 143 (chain A) in PDB entry 3EFC
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 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU 4.0 4.9 + - - -
126A ASP* 3.2 27.3 + - - +
128A THR* 1.3 88.6 - - + +
130A ILE* 1.3 65.0 + - - +
131A ALA 3.3 1.6 - - - -
132A ASP* 3.2 26.2 + - - +
133A ILE* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.9 8.1 - - + -
126A ASP 4.8 1.1 - - - +
127A ARG* 3.3 35.2 - - + +
128A THR 2.8 4.4 + - - +
129A THR* 1.3 76.0 + - - +
131A ALA* 1.3 68.4 + - - +
133A ILE* 3.1 20.0 + - + +
134A GLU* 3.2 15.8 + - - +
153A ALA* 3.4 31.0 - - + +
155A VAL* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR 4.0 5.2 + - - +
129A THR 3.3 0.2 - - - -
130A ILE* 1.3 79.6 - - - +
132A ASP* 1.3 71.1 + - - +
134A GLU* 2.9 26.6 + - - +
135A LYS* 3.2 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 4.7 2.4 - - - +
129A THR* 3.3 33.9 - - + +
131A ALA* 1.3 83.0 - - - +
133A ILE* 1.3 66.7 + - + +
135A LYS* 3.1 7.5 + - - +
136A GLY* 2.9 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.8 23.7 - - + +
117A SER* 6.4 2.0 - - - -
119A VAL* 3.5 30.7 - - + -
125A LEU* 5.2 12.8 - - + +
129A THR* 2.9 30.0 + - - +
130A ILE* 3.1 14.8 + - + +
132A ASP* 1.3 72.2 - - + +
134A GLU* 1.3 67.6 + - + +
136A GLY* 3.2 3.0 + - - -
137A LEU* 3.1 24.7 + - + +
165A LEU* 5.3 7.6 - - + -
167A LEU* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 3.4 7.3 - - - +
131A ALA* 2.9 24.1 + - - +
133A ILE* 1.3 70.7 - - - +
135A LYS* 1.3 56.7 + - + +
136A GLY 2.5 17.2 + - - -
137A LEU* 2.5 10.3 + - - +
138A GLU* 2.5 30.9 + - - +
151A VAL* 3.2 31.6 - - + +
152A LYS* 3.7 2.6 - - - -
153A ALA* 3.0 45.3 + - + +
167A LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ALA* 3.2 26.7 + - + +
132A ASP* 3.1 10.0 + - - +
134A GLU* 1.3 75.3 - - + +
136A GLY* 1.3 56.8 + - - +
138A GLU* 3.5 29.4 - - + +
139A ASP* 2.9 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 4.2 4.7 + - - +
117A SER* 5.3 9.2 - - - -
132A ASP 2.9 9.6 + - - -
133A ILE* 3.6 5.8 - - - -
134A GLU 2.5 7.7 + - - -
135A LYS* 1.3 75.3 - - - +
137A LEU* 1.3 59.2 + - - +
139A ASP* 3.3 6.8 + - - +
140A PHE* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.3 16.2 - - + -
113A ASN* 4.0 18.4 - - - +
114A LEU* 3.9 23.8 - - + -
133A ILE* 3.1 18.5 + - + +
134A GLU 2.5 10.1 + - - +
136A GLY* 1.3 69.6 - - - +
138A GLU* 1.3 60.6 + - - +
139A ASP 2.9 1.6 - - - -
140A PHE* 2.8 21.5 + - + +
141A TYR* 3.0 17.6 + - + +
151A VAL* 3.7 30.1 - - + -
167A LEU* 3.3 32.5 - - + -
169A PHE* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 2.5 16.6 + - - +
135A LYS* 3.5 36.1 - - - +
137A LEU* 1.3 73.8 - - - +
139A ASP* 1.3 61.0 + - - +
141A TYR* 3.5 5.7 + - - +
142A TYR* 3.5 17.3 + - - +
147A TYR 4.8 4.5 - - - +
149A ALA 3.3 26.5 - - - +
150A SER* 3.7 9.3 + - - -
151A VAL* 3.2 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LYS* 2.9 25.1 + - - +
136A GLY* 3.5 8.1 - - - +
137A LEU 2.9 0.6 - - - -
138A GLU* 1.3 79.4 - - - +
140A PHE* 1.3 58.1 + - - +
141A TYR 3.1 2.2 - - - -
142A TYR* 3.4 13.5 - - - +
143A SER* 3.2 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 4.1 18.6 - - + -
109A MET* 4.6 18.8 - - + -
110A LEU* 3.6 28.9 - - + -
113A ASN* 3.0 37.7 - - + +
136A GLY 2.9 8.0 + - - +
137A LEU* 2.8 8.8 + - + +
139A ASP* 1.3 78.1 - - - +
141A TYR* 1.3 65.9 + + - +
143A SER* 2.9 33.2 + - - -
144A VAL* 3.6 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASN* 3.9 18.4 - - - +
105A VAL* 3.2 27.9 - - + +
110A LEU* 4.4 7.9 - - + -
137A LEU* 3.0 17.0 + - - +
138A GLU* 3.9 7.6 - - - +
139A ASP 3.1 0.6 - - - -
140A PHE* 1.3 92.3 - + - +
142A TYR* 1.3 62.6 + - - +
143A SER 3.1 0.4 - - - -
144A VAL* 3.2 12.3 - - + +
146A LYS* 2.8 52.4 + - + -
147A TYR 4.8 0.2 - - - -
149A ALA* 3.8 23.1 - - + -
151A VAL* 5.6 2.9 - - + -
169A PHE* 4.2 23.1 - + - -
171A GLU* 2.9 45.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU 3.5 8.2 + - - +
139A ASP* 3.4 19.3 - - - +
141A TYR* 1.3 74.0 - - - +
143A SER* 1.3 56.8 + - - +
144A VAL 2.9 12.7 + - - -
145A GLY 3.6 6.4 + - - -
147A TYR* 3.5 64.4 + + + +
247A LEU* 4.1 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP 3.2 11.7 + - - -
140A PHE* 2.9 35.4 - - - -
141A TYR 3.1 0.6 - - - -
142A TYR* 1.3 79.2 - - - +
144A VAL* 1.3 56.0 + - - +
211A ASP* 4.9 5.2 - - - +
----------------------------------------------------------
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