Contacts of the helix formed by residues 134 - 146 (chain B) in PDB entry 1RRP
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 PRO 134 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASP* 3.6 38.2 - - + +
108B ARG* 4.4 7.2 - - + -
133B THR* 1.3 87.0 - - - +
135B GLU* 1.3 81.2 + - - +
136B GLU 3.1 1.8 - - - -
137B ALA* 2.9 2.4 + - - +
138B ALA* 2.6 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B THR* 3.7 19.5 - - - +
134B PRO* 1.3 97.7 - - - +
136B GLU* 1.3 59.3 + - + +
138B ALA* 3.4 7.2 + - - +
139B LEU* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 4.3 5.0 - - - -
43B ASN* 3.1 40.3 + - - +
44B ARG* 4.7 2.4 - - - +
131B PHE* 4.0 12.9 - - + -
132B LYS* 3.3 13.9 - - - +
133B THR* 2.7 47.3 + - - +
135B GLU* 1.3 77.0 - - + +
137B ALA* 1.3 65.4 + - - +
139B LEU* 3.5 6.8 + - - +
140B PHE* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASP 3.7 18.4 - - - +
108B ARG* 3.8 11.4 - - - -
110B PHE* 3.4 25.1 - - + -
131B PHE* 3.2 24.1 - - + -
133B THR 3.4 4.2 + - - +
134B PRO 2.9 7.9 + - - +
136B GLU* 1.3 77.5 - - - +
138B ALA* 1.3 54.1 + - - +
140B PHE* 2.9 5.2 + - - +
141B LYS 2.7 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 4.4 0.9 - - - -
134B PRO 2.6 20.4 + - - +
135B GLU* 3.5 9.0 - - - +
137B ALA* 1.3 73.1 - - - +
139B LEU* 1.3 57.0 + - - +
141B LYS* 3.2 11.5 + - - +
142B CYS* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.5 20.0 - - + -
43B ASN* 5.5 6.5 - - + +
135B GLU 2.9 18.1 + - - +
136B GLU* 3.7 7.2 - - - +
138B ALA* 1.3 75.4 - - - +
140B PHE* 1.3 62.9 + - - +
142B CYS* 3.5 8.9 - - + +
143B LYS* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.1 34.2 - + + -
65B VAL* 4.1 20.4 - - + -
67B ILE* 4.2 16.6 - - + -
78B LEU* 3.8 26.7 - - + -
100B LEU* 3.4 31.4 - - + -
110B PHE* 3.8 5.6 - + - -
112B TRP* 5.3 3.6 - + - -
129B ILE* 4.3 17.7 - - + -
131B PHE* 3.4 33.0 - + + -
136B GLU 3.0 7.9 + - - +
137B ALA 2.9 9.0 + - - +
139B LEU* 1.3 77.0 - - - +
141B LYS* 1.3 55.4 + - - +
143B LYS* 4.2 0.2 - - - +
144B PHE* 2.8 43.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.4 23.9 + - + +
110B PHE* 4.0 21.3 - - + -
137B ALA 2.7 15.2 + - - +
138B ALA* 3.3 13.7 - - - +
140B PHE* 1.3 77.9 - - - +
142B CYS* 1.3 68.5 + - - +
144B PHE* 3.3 5.2 - - - +
145B GLU* 2.9 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ALA 2.8 18.6 + - - +
139B LEU* 3.5 11.0 - - + +
141B LYS* 1.3 72.0 - - - +
143B LYS* 1.3 54.8 + - - +
145B GLU* 2.7 17.8 + - - +
146B GLU* 2.7 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.1 34.0 + - + +
41B PHE* 3.5 36.3 - - + +
67B ILE* 4.0 2.6 - - + +
139B LEU* 2.9 30.0 + - + +
142B CYS* 1.3 77.6 - - + +
144B PHE* 1.3 63.8 + - - +
146B GLU* 3.4 33.4 + - - +
147B ALA* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.8 11.1 - - + +
78B LEU* 3.7 23.3 - - + -
92B HIS* 5.4 0.4 - + - -
94B ILE* 3.4 49.7 - - + +
98B MET* 4.5 18.4 - - + -
100B LEU* 3.2 48.7 - - + -
112B TRP* 4.7 8.3 - + - -
140B PHE* 2.8 33.7 + + + +
141B LYS 3.3 3.4 - - - +
143B LYS* 1.3 71.2 - - - +
145B GLU* 1.3 67.2 + - + +
147B ALA* 3.0 24.2 + - - +
148B GLN* 3.5 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 5.9 4.3 - - + +
141B LYS* 2.9 54.1 + - + +
142B CYS* 2.7 14.1 + - - +
144B PHE* 1.3 74.2 - - + +
146B GLU* 1.3 57.0 + - - +
147B ALA 2.9 1.6 - - - -
148B GLN* 2.7 44.0 + - - +
149B SER* 2.9 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.3 28.3 - - + -
142B CYS* 2.7 30.2 + - - +
143B LYS* 3.4 33.8 + - - +
145B GLU* 1.3 72.7 - - - +
147B ALA* 1.3 56.3 + - - +
148B GLN 3.1 0.2 - - - -
149B SER* 3.2 27.5 + - - -
150B ILE* 3.5 12.9 - - + +
----------------------------------------------------------
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