Contacts of the helix formed by residues 191 - 203 (chain A) in PDB entry 1XRE
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 ASN 191 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU 3.4 15.2 + - - +
89A VAL* 2.8 26.0 + - - +
90A MET 4.0 2.4 + - - -
91A SER* 3.9 27.2 + - - -
94A GLY* 4.8 1.6 - - - -
189A THR 3.4 0.8 + - - -
190A VAL* 1.3 71.9 - - - +
192A TRP* 1.3 57.5 + - - +
193A ASP* 3.4 13.2 + - - +
194A ARG* 3.1 33.9 + - - +
195A VAL* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 3.5 22.1 + - - -
96A GLY 3.1 16.6 + - - -
97A GLU 3.6 10.7 - - - -
98A PRO* 3.7 29.8 - - + -
99A ASN* 3.6 23.3 - - - +
102A VAL* 4.9 4.1 - - + +
106A ILE* 4.1 10.8 - - + -
113A PHE* 3.4 34.1 - + - -
116A LEU* 4.6 7.2 - - + -
135A LEU* 5.2 0.9 - - + -
162A LEU* 4.0 19.7 - - + -
187A TRP* 4.1 11.3 + + - -
190A VAL* 3.4 27.0 + - + +
191A ASN* 1.3 68.9 + - - +
193A ASP* 1.3 66.4 + - - +
195A VAL* 3.8 33.1 - - + +
196A ASN* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 3.4 23.4 + - - +
191A ASN* 3.2 10.2 + - - +
192A TRP* 1.3 80.5 - - - +
194A ARG* 1.3 62.2 + - - +
196A ASN* 3.4 4.6 + - - +
197A GLU* 3.2 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.4 28.1 + - - -
87A TRP 5.0 0.8 + - - -
88A GLU* 2.9 69.3 + - + +
89A VAL* 4.5 4.3 - - + -
90A MET 5.4 0.8 + - - -
191A ASN* 3.1 25.2 + - - +
193A ASP* 1.3 76.9 - - - +
195A VAL* 1.3 66.3 + - - +
197A GLU* 3.1 27.5 + - - +
198A LYS* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.3 6.5 - - + -
102A VAL* 4.5 14.8 - - + -
135A LEU* 4.9 4.0 - - + -
161A LEU* 3.8 37.6 - - + +
162A LEU* 3.9 25.4 - - + -
190A VAL* 4.5 0.9 - - + -
191A ASN 3.1 15.7 + - - +
192A TRP* 3.8 35.4 - - + +
194A ARG* 1.3 76.3 - - - +
196A ASN* 1.3 62.9 + - - +
198A LYS* 3.1 5.2 + - - +
199A TYR* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 4.2 11.5 - - - +
100A GLY* 4.2 4.3 - - - -
101A ASP* 3.2 21.8 + - - +
102A VAL* 3.0 45.2 - - + +
192A TRP 3.0 19.0 + - - +
193A ASP* 3.6 6.5 - - - +
195A VAL* 1.3 76.0 - - - +
197A GLU* 1.3 62.0 + - - +
199A TYR* 3.3 3.5 + - - +
200A LEU* 3.1 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASP* 3.2 23.9 + - - +
194A ARG* 3.1 28.6 + - + +
196A ASN* 1.3 74.3 - - - +
198A LYS* 1.3 65.6 + - + +
200A LEU* 3.5 10.7 + - + +
201A GLN* 3.1 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.0 21.4 - - + +
88A GLU* 2.8 31.6 + - - -
89A VAL* 5.2 0.2 - - + -
159A ILE* 5.3 1.2 - - - +
160A PRO 4.5 6.9 - - - +
161A LEU* 3.8 31.0 - - + +
194A ARG* 2.9 33.3 + - + +
195A VAL* 3.1 7.4 + - - +
197A GLU* 1.3 76.1 - - + +
199A TYR* 1.3 57.7 + - - +
201A GLN* 3.5 23.4 + - - +
202A ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP* 4.8 9.6 - - + -
102A VAL* 3.8 33.0 - - + -
105A VAL* 3.8 34.1 - - + +
137A LEU* 3.8 27.3 - - + +
140A GLU 5.0 2.3 + - - -
142A LEU* 4.3 1.6 - - + -
161A LEU* 3.9 27.3 - - + +
195A VAL 2.9 12.3 + - - +
196A ASN* 3.6 8.1 - - - +
197A GLU 3.3 0.4 - - - -
198A LYS* 1.3 75.1 - - - +
200A LEU* 1.3 76.2 + - + +
202A ALA* 3.0 12.0 + - - +
203A ILE* 3.1 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP* 3.8 32.8 - - + +
196A ASN* 3.1 33.1 + - - +
197A GLU* 3.9 9.2 - - + +
199A TYR* 1.3 76.6 - - + +
201A GLN* 1.3 66.9 + - - +
203A ILE* 3.2 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLU 3.1 17.5 + - - +
198A LYS* 3.5 29.8 + - - +
200A LEU* 1.3 76.5 - - - +
202A ALA* 1.3 64.2 + - - +
203A ILE 3.8 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.6 22.9 - - + +
159A ILE* 3.8 39.9 - - + +
161A LEU* 4.2 4.3 - - + -
198A LYS 2.9 16.6 + - - +
199A TYR* 3.0 12.3 + - - +
201A GLN* 1.3 78.4 - - - +
203A ILE* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 4.0 18.8 - - + -
140A GLU* 6.5 1.1 - - - -
199A TYR* 3.1 39.5 + - + +
200A LEU* 3.2 38.8 - - + +
201A GLN 3.8 5.0 - - - +
202A ALA* 1.3 79.9 - - - +
----------------------------------------------------------
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