Contacts of the helix formed by residues 133 - 145 (chain A) in PDB entry 1WD5
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 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.3 26.4 - - - +
131A ALA 4.5 0.2 - - - +
132A THR* 1.3 77.8 + - - +
134A ALA* 1.3 64.8 + - - +
135A SER 3.4 2.2 - - - -
136A MSE 3.3 7.9 + - - +
137A GLU* 2.9 33.3 + - - +
162A ALA* 4.5 2.7 - - - -
165A ARG* 6.0 0.4 - - - -
166A LEU* 4.8 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 4.4 26.6 - - - +
64A GLU* 5.6 8.7 - - - +
132A THR* 3.3 15.9 + - - +
133A GLY* 1.3 77.5 - - - +
135A SER* 1.3 64.6 + - - +
137A GLU* 3.4 7.3 + - - +
138A ALA* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.0 16.8 - - - +
54A VAL* 4.5 5.3 - - - +
56A LYS* 5.8 1.8 - - - -
127A ASP* 5.6 1.8 - - - -
133A GLY 3.4 0.4 - - - -
134A ALA* 1.3 78.4 - - - +
136A MSE 1.3 58.3 + - - +
138A ALA* 3.2 8.9 + - - +
139A ALA* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.0 27.6 - - + +
125A LEU* 3.7 36.8 - - - +
126A VAL 4.3 0.4 - - - -
127A ASP* 4.1 13.7 - - + -
130A VAL* 4.6 6.1 - - + -
133A GLY* 3.3 11.7 + - - +
135A SER* 1.3 78.8 - - - +
137A GLU* 1.3 58.2 + - - +
139A ALA* 3.1 3.8 + - - +
140A LEU* 2.9 27.4 + - + +
153A VAL* 4.1 15.0 - - + -
155A VAL* 4.1 26.2 - - + -
166A LEU* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 6.1 6.5 - - + -
133A GLY 2.9 22.1 + - - +
134A ALA* 3.7 6.9 - - - +
136A MSE 1.3 76.2 - - - +
138A ALA* 1.3 62.8 + - - +
140A LEU* 3.2 4.2 + - - +
141A SER* 3.0 27.1 + - - -
165A ARG* 3.5 38.6 - - + +
166A LEU* 3.8 18.4 - - + -
169A ARG* 3.3 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.1 12.6 - - + -
55A ARG* 5.0 0.2 - - - -
56A LYS* 4.1 23.6 - - + +
68A GLY 5.1 0.9 - - - +
69A ALA* 3.8 23.9 - - + +
134A ALA 3.2 9.8 + - - +
135A SER* 3.2 11.3 + - - +
137A GLU* 1.3 77.6 - - - +
139A ALA* 1.3 63.9 + - - +
141A SER* 3.3 5.6 + - - -
142A VAL* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.5 6.3 - - + -
52A VAL* 4.1 22.4 - - + -
54A VAL* 3.8 15.5 - - + +
125A LEU* 4.2 16.2 - - + -
135A SER 2.9 14.4 + - - +
136A MSE 3.3 12.6 - - - +
138A ALA* 1.3 78.5 - - - +
140A LEU* 1.3 55.9 + - - +
142A VAL* 3.4 1.4 + - - +
143A VAL* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 3.4 23.3 - - + -
136A MSE 2.9 13.1 + - - +
137A GLU* 3.5 9.9 - - - +
139A ALA* 1.3 77.8 - - - +
141A SER* 1.3 62.6 + - - +
143A VAL* 4.6 1.6 - - + -
144A PHE* 2.9 46.0 + - + -
151A VAL* 3.7 20.9 - - + -
153A VAL* 3.9 18.4 - - + -
166A LEU* 4.0 28.5 - - + +
169A ARG* 4.1 32.3 - - + +
170A ALA* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 5.6 0.9 - - - -
69A ALA* 4.3 14.6 - - - -
77A VAL* 3.7 11.4 - - - +
79A MSE 3.4 23.3 - - - +
137A GLU 3.0 11.4 + - - -
138A ALA* 3.3 10.0 + - - -
140A LEU* 1.3 79.2 - - - +
142A VAL* 1.3 61.4 + - - +
144A PHE* 3.8 4.4 + - - +
145A GLN* 3.5 22.3 + - - +
169A ARG* 2.8 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 6.0 0.2 - - + -
54A VAL* 3.6 29.2 - - + -
69A ALA* 4.1 12.1 - - + -
70A VAL 4.1 5.2 - - - -
71A GLY* 4.0 18.8 - - - +
75A GLU* 3.6 23.8 - - + +
77A VAL* 4.5 12.3 - - + -
118A ARG* 5.3 2.9 - - - +
138A ALA 3.2 13.6 + - - +
139A ALA 3.9 2.2 - - - +
141A SER* 1.3 74.6 - - - +
143A VAL* 1.3 68.0 + - + +
145A GLN* 3.1 15.1 + - - +
146A GLU* 3.3 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.1 21.5 - - + -
52A VAL* 4.3 9.2 - - + -
118A ARG* 4.7 3.1 - - + +
123A VAL* 4.2 22.2 - - + -
125A LEU* 4.2 11.9 - - + -
139A ALA 2.9 24.2 + - - +
140A LEU* 3.9 4.9 - - - +
142A VAL* 1.3 76.3 - - + +
144A PHE* 1.3 57.9 + - + +
146A GLU* 2.9 36.7 + - + +
148A PRO* 3.2 25.7 - - + +
151A VAL* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 2.9 41.9 + - + +
141A SER* 4.0 4.3 - - - +
142A VAL 3.3 0.2 - - - -
143A VAL* 1.3 76.3 - - + +
145A GLN* 1.3 67.7 + - + +
146A GLU 3.1 1.5 + - - -
147A GLY* 3.6 8.7 + - - -
148A PRO* 3.9 7.0 - - + +
151A VAL* 3.6 31.0 - - + -
169A ARG* 3.6 44.0 - - + -
170A ALA* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 6.3 1.3 - - + -
77A VAL* 3.8 30.3 - - + +
141A SER 3.5 16.4 + - - +
142A VAL* 3.1 9.4 + - + +
144A PHE* 1.3 82.6 - - - +
146A GLU* 1.3 61.0 + - + +
147A GLY 3.3 2.4 + - - -
----------------------------------------------------------
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