Contacts of the helix formed by residues 136 - 151 (chain A) in PDB entry 1URP
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 SER 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP 5.7 1.2 + - - -
90A ARG* 6.0 0.7 - - - -
91A GLN* 5.0 21.5 + - - +
105A ASN* 5.1 0.2 - - - -
134A GLY 3.8 1.6 + - - -
135A THR* 1.3 72.9 - - - +
137A ALA* 1.3 57.4 + - - +
139A ARG* 3.3 24.4 + - - +
140A GLU* 2.9 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN* 4.0 14.6 - - - +
135A THR* 3.3 4.3 - - - +
136A SER* 1.3 79.9 + - - +
138A ALA* 1.3 57.4 + - - +
141A ARG* 2.9 65.5 + - - +
164A PHE* 4.0 13.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
130A GLN* 5.2 2.2 - - + -
131A GLY* 3.9 16.4 - - - +
132A ILE 3.5 14.4 - - - +
133A ALA* 5.3 1.8 - - - -
134A GLY 5.5 0.7 - - - +
135A THR* 3.3 20.4 + - - +
137A ALA* 1.3 78.6 - - - +
139A ARG* 1.3 56.9 + - - +
142A GLY* 3.0 24.1 + - - -
164A PHE* 3.9 3.2 - - - -
189A GLN* 3.2 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 4.9 9.9 + - - +
134A GLY 4.5 9.8 + - - -
135A THR 3.3 12.0 + - - +
136A SER* 3.7 26.6 - - - +
137A ALA 3.3 1.0 - - - -
138A ALA* 1.3 79.1 - - - +
140A GLU* 1.3 81.6 + - - +
142A GLY* 3.3 2.3 + - - -
143A GLU* 3.0 34.3 + - + +
260A LYS* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 4.6 7.3 - - - +
100A HIS* 6.0 0.2 + - - -
102A ALA* 5.8 2.1 - - - +
103A SER 4.3 6.2 - - - +
105A ASN* 3.4 34.3 + - + +
106A VAL* 3.4 24.1 + - + +
136A SER* 2.9 28.2 + - - +
139A ARG* 1.3 95.7 + - - +
141A ARG* 1.3 66.4 + - - +
143A GLU* 3.3 13.4 + - - +
144A GLY 3.0 19.2 + - - -
260A LYS* 4.7 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN* 2.7 42.5 + - + +
109A GLY* 3.8 5.5 - - - -
137A ALA* 2.9 37.6 + - - +
140A GLU* 1.3 76.0 - - - +
142A GLY* 1.3 56.5 + - - +
144A GLY 3.4 0.7 + - - -
145A PHE* 3.0 29.1 + - - +
164A PHE* 4.0 10.1 - - - -
187A PHE* 4.2 6.8 - - + -
189A GLN* 2.7 56.7 + - + -
190A ASN* 4.2 1.0 - - - +
214A PHE* 3.3 35.7 - - + -
215A ASP* 3.4 26.3 + - - -
235A GLN* 3.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 3.9 7.6 - - - +
138A ALA 3.0 15.9 + - - -
139A ARG 3.6 1.3 - - - -
141A ARG* 1.3 77.6 - - - +
143A GLU* 1.3 56.4 + - - +
145A PHE* 3.3 4.0 + - - +
146A GLN* 3.0 32.9 + - - +
189A GLN* 3.5 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 4.0 25.6 - - + +
139A ARG* 3.0 22.6 + - + +
140A GLU* 3.5 16.6 - - - +
142A GLY* 1.3 71.0 - - - +
144A GLY* 1.3 68.3 + - - +
146A GLN* 3.1 10.7 + - + +
147A GLN* 3.0 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.0 36.1 - - - -
110A LYS* 3.2 23.5 - - - -
140A GLU 3.0 11.3 + - - -
141A ARG 3.8 3.1 - - - -
143A GLU* 1.3 78.8 - - - +
145A PHE* 1.3 60.7 + - - +
147A GLN* 3.1 16.6 + - - +
148A ALA 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLY 3.5 15.9 - - - +
113A GLY* 4.0 20.6 - - - -
116A ILE* 4.3 4.5 - - + -
126A VAL* 3.9 30.1 - - + -
127A ILE 5.3 0.4 - - - -
128A GLU* 3.5 45.3 - - + +
141A ARG 3.0 14.0 + - - +
142A GLY 3.7 1.8 - - - +
143A GLU 3.3 0.2 - - - -
144A GLY* 1.3 76.6 - - - +
146A GLN* 1.3 59.8 + - - +
148A ALA* 3.0 5.2 + - - +
149A VAL* 2.8 45.6 + - + +
154A PHE* 4.2 10.1 - + - -
156A VAL* 4.5 4.9 - - + -
187A PHE* 3.6 37.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 4.1 17.6 + - - -
142A GLY 3.0 18.0 + - - +
143A GLU* 3.1 13.4 + - + +
145A PHE* 1.3 76.8 - - - +
147A GLN* 1.3 62.9 + - - +
149A VAL* 3.1 28.4 + - - +
150A ALA* 2.9 24.6 + - - +
156A VAL* 4.8 9.4 - - - +
159A SER* 5.5 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.5 30.1 - - - +
107A LEU* 5.9 0.3 - - - -
110A LYS* 3.6 30.2 - - + +
143A GLU* 3.0 25.7 + - - +
144A GLY* 3.1 6.7 + - - +
146A GLN* 1.3 75.4 - - - +
148A ALA* 1.3 55.8 + - - +
150A ALA* 3.4 5.0 + - - +
151A ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 3.8 18.0 - - - +
113A GLY* 3.5 37.9 - - - -
114A ASP* 3.9 6.5 - - - +
144A GLY 3.4 1.6 + - - -
145A PHE 3.0 8.8 + - - +
147A GLN* 1.3 75.0 - - - +
149A VAL* 1.3 60.5 + - - +
151A ALA* 4.6 1.3 - - - -
152A HIS* 2.8 41.6 + - + +
154A PHE* 3.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 2.8 46.0 + - + +
146A GLN* 3.1 26.2 + - - +
148A ALA* 1.3 75.9 - - - +
150A ALA* 1.3 57.8 + - - +
153A LYS* 2.9 9.7 + - - -
154A PHE* 2.9 55.6 + - + +
156A VAL* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLN 2.9 14.7 + - - +
147A GLN* 3.8 5.4 - - - +
149A VAL* 1.3 75.0 - - - +
151A ALA* 1.3 68.0 + - - +
153A LYS* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 5.1 9.0 - - - +
122A GLU* 3.6 9.2 - - - +
147A GLN 3.0 17.9 + - - +
148A ALA* 4.3 2.2 - - - +
150A ALA* 1.3 77.2 - - - +
152A HIS* 1.3 74.1 + - + +
153A LYS* 3.6 7.4 + - - +
----------------------------------------------------------
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