Contacts of the helix formed by residues 132 - 142 (chain I) in PDB entry 3DV0
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 132 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 3.7 31.2 - - + -
282B LEU* 3.6 22.8 - - + +
284D LEU* 3.6 24.2 - - + +
285D GLU* 4.0 12.3 - - + +
286D ALA* 3.3 38.6 - - - +
324D PHE* 4.2 9.2 - - - -
131I ALA* 1.3 77.5 - - - +
133I PRO* 1.3 75.2 - - + +
134I SER* 4.2 9.9 - - - +
135I VAL* 3.1 20.8 + - + +
136I ARG* 3.2 9.2 + - - +
157I ARG* 5.0 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 133 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 3.9 24.9 - - + +
284B LEU* 3.5 25.1 - - + +
285B GLU 4.7 8.7 - - - +
286B ALA* 5.4 0.4 - - - -
281D ILE* 3.6 51.4 - - + +
282D LEU* 3.7 4.9 - - + -
131I ALA 3.7 0.2 - - - -
132I MET* 1.3 91.8 - - + +
134I SER* 1.3 63.0 + - - +
136I ARG* 3.4 3.9 + - + +
137I LYS* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ILE 4.4 0.6 + - - -
282D LEU* 3.1 41.6 - - - +
283D SER* 5.1 0.9 - - - -
284D LEU 4.0 14.3 + - - -
285D GLU* 4.8 9.0 + - - -
132I MET* 3.2 2.6 - - - +
133I PRO* 1.3 78.7 - - - +
135I VAL* 1.3 71.8 + - - +
137I LYS* 4.0 1.6 - - - +
138I TYR* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I ALA* 3.8 10.3 - - + -
132I MET* 3.1 21.9 + - + +
134I SER* 1.3 83.9 + - - +
136I ARG* 1.3 53.5 + - - +
138I TYR* 2.8 9.7 + - - +
139I ALA* 2.7 33.4 + - - +
146I ILE* 4.6 1.6 - - + -
157I ARG* 6.3 0.7 - - + -
158I VAL* 3.5 29.2 - - + +
159I LEU* 4.2 2.7 - - + -
160I LYS* 3.8 23.1 - - - +
163I ILE* 3.4 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU 3.0 15.7 + - - -
283B SER* 3.8 13.2 + - - +
284B LEU 3.5 21.9 + - - -
285B GLU* 3.2 40.9 + - - +
129I VAL* 2.7 52.6 - - - +
131I ALA* 2.8 32.7 + - + +
132I MET 3.2 6.0 + - - +
133I PRO* 3.8 5.6 - - + +
135I VAL* 1.3 79.9 - - - +
137I LYS* 1.3 61.0 + - - +
139I ALA* 3.3 8.5 + - - +
140I ARG* 2.9 28.6 + - - +
146I ILE* 4.6 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG* 5.2 7.5 - - - +
285B GLU* 3.4 23.0 + - - +
324B PHE* 3.5 45.8 - - + +
282D LEU* 3.7 25.8 - - + -
133I PRO 2.9 19.8 + - - +
134I SER 4.4 0.4 - - - +
136I ARG* 1.3 75.8 + - - +
138I TYR* 1.3 56.4 + - - +
140I ARG* 4.0 16.3 - - + +
141I GLU* 2.7 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I SER 3.2 15.6 + - - +
135I VAL* 2.8 10.0 + - - +
137I LYS* 1.3 75.8 - - - +
139I ALA* 1.3 71.6 + - - +
141I GLU* 3.3 14.4 + - - +
142I LYS* 3.1 65.1 + - + +
160I LYS* 4.2 13.9 - - - -
163I ILE* 4.4 22.0 - - + -
164I ASP* 2.5 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I VAL 2.7 12.5 + - - +
136I ARG 3.4 8.5 - - - +
138I TYR* 1.3 77.3 - - - +
140I ARG* 1.3 55.5 + - - +
142I LYS* 3.3 1.6 + - - -
143I GLY 2.9 8.7 + - - -
144I VAL* 2.7 47.1 + - - +
146I ILE* 3.7 17.7 - - + -
163I ILE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ARG 2.9 17.8 + - - +
137I LYS* 4.2 21.1 - - + +
139I ALA* 1.3 71.5 - - - +
141I GLU* 1.3 60.6 + - - +
143I GLY* 2.7 25.9 + - - +
144I VAL 4.4 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D LEU* 5.6 2.3 - - - +
137I LYS* 2.7 40.0 + - + +
138I TYR* 3.3 16.2 + - - +
140I ARG* 1.3 78.3 - - - +
142I LYS* 1.3 70.5 + - + +
143I GLY* 2.8 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I TYR* 3.1 58.0 + - + +
139I ALA* 4.9 0.4 - - - -
141I GLU* 1.3 89.9 + - - +
143I GLY* 1.3 61.1 + - - +
144I VAL* 3.2 23.2 + - + +
163I ILE* 5.3 0.2 - - + -
167I LEU* 3.9 25.9 - - + +
----------------------------------------------------------
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