Contacts of the helix formed by residues 131 - 142 (chain A) in PDB entry 4X5O
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 LEU 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 5.4 0.2 - - - +
128A ARG* 4.2 20.4 - - - +
130A ASP* 1.3 81.3 + - - +
132A THR* 1.3 57.2 + - - +
133A VAL 3.5 1.1 - - - -
134A PRO* 3.3 7.8 - - - +
135A PHE* 3.1 23.0 + - - +
149A ARG* 3.9 12.0 + - - +
151A HIS* 3.4 53.3 + - + +
153A ALA* 4.2 14.1 - - + +
155A VAL* 4.1 12.8 - - + -
173A GLN* 3.4 24.2 - - + +
175A ASP* 3.2 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP* 2.2 36.0 + - - +
131A LEU* 1.3 76.8 - - - +
133A VAL* 1.3 60.7 + - - +
135A PHE* 3.2 12.8 + - + +
136A ALA* 2.9 29.5 + - - +
149A ARG* 5.6 1.6 - - - +
175A ASP* 4.8 10.3 - - - +
177A ASP* 5.0 5.4 - - - +
330A TYR* 3.7 28.2 + - - +
363A TYR* 3.8 21.1 - - + +
366A LEU* 4.7 15.6 - - - +
367A VAL* 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 5.5 1.8 - - + +
102A THR* 3.7 28.7 - - + +
103A LEU* 4.0 17.7 - - + -
129A TYR* 3.7 29.2 - - + +
130A ASP* 4.0 10.9 + - + +
132A THR* 1.3 74.3 - - - +
134A PRO* 1.4 67.8 - - + +
136A ALA* 3.3 5.9 + - - +
137A ARG* 2.9 26.7 + - - +
366A LEU* 6.2 5.4 - - + -
370A PHE* 4.0 18.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 3.6 32.8 - - + +
95A PRO 5.6 0.4 - - - +
98A GLU* 3.2 35.2 - - + +
103A LEU* 5.3 2.0 - - + -
128A ARG* 4.6 8.1 - - + -
130A ASP 3.3 24.2 - - - +
131A LEU* 3.3 10.8 - - - +
133A VAL* 1.4 94.3 - - + +
135A PHE* 1.3 50.1 + - - +
137A ARG* 3.2 7.9 + - - +
138A TYR* 2.6 36.9 + - - +
151A HIS* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 4.2 10.3 - - + -
94A THR* 5.1 0.4 - - - +
131A LEU 3.1 15.4 + - - +
132A THR* 3.2 15.9 + - + +
134A PRO* 1.3 76.5 - - - +
136A ALA* 1.3 56.0 + - - +
138A TYR* 3.1 7.8 + + - +
139A LEU* 2.9 47.9 + - + +
147A ILE* 3.6 32.1 - - + -
149A ARG* 3.4 46.7 - - + +
177A ASP* 3.9 25.4 - - + -
179A ALA* 4.5 2.7 - - + -
363A TYR* 4.6 5.6 - - - -
367A VAL* 4.5 11.2 - - + -
379A CYS* 4.2 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR 2.9 15.8 + - - +
133A VAL* 3.9 1.1 - - - +
135A PHE* 1.3 73.2 - - - +
137A ARG* 1.3 64.5 + - - +
139A LEU* 3.8 0.9 + - - +
140A ALA* 3.4 22.5 + - - +
366A LEU* 4.3 3.6 - - + +
367A VAL* 3.4 46.5 - - + +
370A PHE* 3.4 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 3.8 14.3 - - - +
95A PRO* 4.2 3.8 - - - +
98A GLU* 2.8 39.7 + - - +
102A THR* 4.4 16.4 - - + -
133A VAL 2.9 17.0 + - - +
134A PRO* 3.5 13.0 + - + +
136A ALA* 1.3 76.0 - - - +
138A TYR* 1.3 61.7 + - - +
140A ALA* 3.3 4.5 + - - +
141A MET* 2.8 60.7 + - - +
370A PHE* 4.5 7.8 - - + -
56B LEU* 4.3 17.9 - - + -
57B LYS 4.6 11.9 - - - +
58B THR* 4.5 8.1 - - - -
64B ASP* 3.0 41.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 3.7 39.7 - - + -
93A ASP 5.9 0.2 - - - -
94A THR* 5.5 0.2 - - + -
134A PRO 2.6 21.3 + - - +
135A PHE* 3.1 10.7 + + - +
137A ARG* 1.3 84.3 - - - +
139A LEU* 1.3 72.6 + - + +
141A MET* 3.4 0.6 + - - -
142A ASN* 2.7 57.9 + - - +
144A LEU* 4.1 22.2 - - + +
147A ILE* 4.2 6.2 - - + +
64B ASP* 3.9 30.3 - - + -
65B TYR 4.8 5.2 - - - -
66B SER* 3.7 11.2 - - - -
67B PRO* 3.3 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 2.9 34.0 + - + +
136A ALA 4.3 3.6 - - - +
138A TYR* 1.3 88.3 - - + +
140A ALA* 1.3 57.4 + - - +
143A LYS* 3.0 4.6 + - - -
144A LEU* 2.7 72.0 + - + +
146A ASN 5.4 1.1 - - - +
147A ILE* 3.7 17.7 - - + -
179A ALA* 4.0 17.3 - - + -
367A VAL* 3.6 27.4 - - + +
377A VAL* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA 3.4 17.3 + - - +
137A ARG 3.3 1.5 + - - +
138A TYR 3.1 0.4 - - - -
139A LEU* 1.3 78.2 - - - +
141A MET* 1.3 61.5 + - - +
142A ASN 3.0 5.5 + - - -
143A LYS* 3.3 18.4 + - - +
367A VAL 5.7 0.7 - - - +
370A PHE* 3.8 18.4 - - + +
371A ASP* 4.7 6.1 - - + +
372A PRO* 5.8 3.3 - - + +
54B PHE* 5.2 5.2 - - - -
56B LEU* 3.6 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 2.8 44.4 + - - +
138A TYR* 3.4 4.2 + - - +
140A ALA* 1.3 74.7 - - - +
142A ASN* 1.3 66.8 + - - +
143A LYS* 5.2 4.1 + - - +
54B PHE* 5.7 4.7 - - + -
56B LEU* 3.7 42.0 - - + +
57B LYS* 4.0 1.1 - - - -
58B THR* 3.8 34.1 - - + +
64B ASP* 4.5 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 2.7 59.6 + - - +
140A ALA 3.0 0.2 - - - -
141A MET* 1.3 87.4 - - - +
143A LYS* 1.3 73.7 + - - +
144A LEU* 3.5 22.5 + - + +
64B ASP* 5.1 1.8 + - - -
----------------------------------------------------------
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