Contacts of the helix formed by residues 133 - 150 (chain A) in PDB entry 4RUH
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 ASP 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY* 3.6 5.0 - - - -
99A HIS* 3.1 61.0 + - + +
102A VAL* 4.4 4.6 - - - +
129A GLY* 3.5 1.6 + - - -
131A THR 3.6 1.3 - - - +
132A ASP* 1.3 70.6 + - - +
134A LYS* 1.3 66.0 + - - +
135A GLY 3.5 2.5 - - - -
136A PRO* 3.4 11.6 - - - +
137A VAL* 3.2 27.1 + - - +
194A SER 2.9 22.8 - - - +
195A ASP* 3.0 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 11.2 - - + -
25A TRP* 2.6 59.7 + - + +
26A VAL* 4.0 11.0 + - + +
28A ILE 2.7 23.8 + - - -
30A SER* 3.1 21.8 + - - +
44A MET* 4.1 8.1 - - - -
100A LEU* 3.4 20.9 - - + +
102A VAL* 3.9 17.8 - - + +
116A PHE* 5.8 0.4 - - - -
128A ARG 5.1 2.1 + - - -
129A GLY* 2.8 17.2 + - - +
133A ASP* 1.3 79.6 - - - +
135A GLY* 1.3 57.5 + - - +
137A VAL* 4.6 2.7 - - - -
138A ALA* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.4 14.8 - - - +
130A SER 3.2 19.4 + - - -
134A LYS* 1.3 77.9 - - - +
136A PRO* 1.3 56.5 - - - +
138A ALA* 3.1 1.6 + - - -
139A GLY* 2.7 31.5 + - - -
451A LEU* 4.2 3.1 - - - -
456A TYR* 3.3 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER 4.0 0.9 - - - +
131A THR* 3.4 33.2 - - - +
133A ASP* 3.4 15.3 - - - +
135A GLY* 1.3 88.7 - - - +
137A VAL* 1.3 55.7 + - - +
139A GLY* 3.1 5.7 + - - +
140A TRP* 3.0 31.1 + - - -
194A SER* 3.3 37.0 - - - +
195A ASP* 5.3 1.1 - - - -
196A ASN 5.8 2.5 - - - +
437A VAL* 4.3 26.2 - - + +
438A GLY 5.5 0.4 - - - +
451A LEU* 4.8 2.7 - - + -
456A TYR* 5.6 0.2 - - + -
463A LEU* 3.7 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TRP* 3.7 19.5 - - + -
98A GLY* 4.2 16.6 - - - -
99A HIS 4.3 6.5 - - - +
100A LEU* 4.1 12.6 - - + -
133A ASP* 3.2 38.2 + - - +
134A LYS* 4.0 3.6 - - - +
135A GLY 3.2 0.4 - - - -
136A PRO* 1.3 74.2 - - - +
138A ALA* 1.3 65.5 + - - +
140A TRP* 3.0 26.5 + - + +
141A ILE* 3.3 14.6 + - + +
160A PHE* 6.0 1.3 - - + -
162A LEU* 4.3 24.5 - - + -
194A SER 5.0 2.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
21A LYS* 4.3 12.3 - - + +
22A LEU* 5.1 5.4 - - + -
25A TRP* 3.6 25.0 - - + -
134A LYS 2.8 19.6 + - - +
135A GLY* 3.5 5.2 - - - +
137A VAL* 1.3 75.2 - - - +
139A GLY* 1.3 63.9 + - - +
141A ILE* 3.1 5.4 + - - +
142A ASN* 2.9 31.1 + - - +
456A TYR* 3.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY 2.7 15.1 + - - -
136A PRO* 3.1 9.6 + - - -
138A ALA* 1.3 76.7 - - - +
140A TRP* 1.3 55.2 + - - +
142A ASN* 3.5 3.5 + - - +
143A ALA* 2.9 29.5 + - - +
437A VAL* 6.4 0.2 - - - -
456A TYR* 4.2 2.9 - - - -
459A GLY 5.9 0.2 - - - -
460A THR* 3.6 23.6 - - - +
463A LEU* 3.8 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 3.5 50.7 - - + +
97A TYR 4.9 2.7 + - - -
136A PRO 3.0 23.0 + - - -
137A VAL* 3.0 21.9 + - + +
139A GLY* 1.3 74.1 - - - +
141A ILE* 1.3 65.1 + - - +
143A ALA* 3.1 5.4 + - + +
144A LEU* 3.0 28.4 + - - +
160A PHE* 4.6 12.3 - + + -
192A CYS* 3.7 40.8 - - + -
194A SER* 3.6 24.2 - - - +
463A LEU* 3.8 39.3 - - + -
466A TYR* 3.9 11.9 - + - -
467A LEU* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 4.1 11.0 - - - -
25A TRP* 4.2 17.9 - - + -
48A ALA* 5.3 2.9 - - + +
51A ASP* 4.1 29.4 - - + +
52A VAL* 4.4 13.9 - - + -
55A LEU* 4.3 20.3 - - + +
137A VAL* 3.5 15.5 - - + +
138A ALA 3.1 6.0 + - - +
140A TRP* 1.3 75.4 - - - +
142A ASN* 1.3 53.5 + - - +
144A LEU* 3.2 3.3 + - - +
145A GLU* 2.8 38.1 + - + +
160A PHE* 3.7 30.5 - - + -
162A LEU* 5.7 3.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
17A ARG* 5.5 0.7 + - - -
18A TYR* 3.4 45.1 + - + +
21A LYS* 3.3 23.3 - - - +
138A ALA* 2.9 27.0 + - - +
139A GLY* 4.1 1.8 - - - +
141A ILE* 1.3 73.3 - - - +
143A ALA* 1.3 56.4 + - - +
145A GLU* 3.8 9.3 - - - +
146A ALA* 3.0 28.4 + - - +
456A TYR* 3.0 29.7 + - - -
460A THR* 3.8 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLY 2.9 19.1 + - - +
140A TRP* 3.1 6.5 + - - +
142A ASN* 1.3 75.5 - - - +
144A LEU* 1.3 65.6 + - - +
146A ALA* 3.1 20.4 + - - +
147A TYR* 3.5 15.9 - - - -
460A THR* 3.7 12.3 - - - +
463A LEU* 4.2 7.2 - - + -
464A ALA* 3.8 32.1 - - - +
467A LEU* 4.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.7 25.1 - - + -
85A LEU* 3.9 4.3 - - + -
96A ILE* 4.8 4.3 - - + -
140A TRP* 3.0 18.1 + - + +
141A ILE 3.7 1.3 - - - +
143A ALA* 1.3 72.1 - - - +
145A GLU* 1.3 65.8 + - - +
146A ALA 3.3 0.2 + - - -
147A TYR* 3.4 17.7 + - - +
148A GLN* 3.6 14.4 + - - +
154A ILE* 3.5 36.6 - - + +
158A VAL* 3.7 17.5 - - + -
160A PHE* 3.3 39.9 - - + -
467A LEU* 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 4.9 0.4 - - - +
17A ARG* 2.8 42.6 + - - -
18A TYR* 4.1 8.3 + - - -
55A LEU* 4.1 21.3 - - + +
141A ILE* 2.8 24.3 + - + +
142A ASN* 3.8 7.9 - - - +
144A LEU* 1.3 72.7 - - - +
146A ALA* 1.3 58.0 + - - +
148A GLN* 3.2 5.9 + - + +
149A LYS* 2.8 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.8 14.6 - - + +
10A TYR* 4.1 21.3 - - + -
11A ILE* 4.2 22.7 - - + -
18A TYR* 4.6 0.2 - - - +
142A ASN 3.0 14.8 + - - +
143A ALA* 3.1 13.2 + - - +
145A GLU* 1.3 76.9 - - - +
147A TYR* 1.3 54.4 - - - +
149A LYS* 3.7 0.5 - - - +
150A THR* 2.6 39.9 + - - +
464A ALA* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 5.2 2.2 - - + -
7A LEU* 3.4 30.2 - - + +
143A ALA 3.5 23.3 + - - -
144A LEU* 3.4 11.8 + - - +
145A GLU 3.2 0.2 - - - -
146A ALA* 1.3 77.8 - - - +
148A GLN* 1.3 62.8 + - - +
150A THR* 2.7 19.7 + - - -
152A GLN* 2.9 36.0 + - + +
153A GLU 3.8 13.7 - - - -
154A ILE* 4.0 20.0 - - + +
155A PRO* 3.5 30.1 - - + +
464A ALA* 2.7 33.7 + - + -
467A LEU* 4.4 7.2 - - + -
468A TYR* 3.3 22.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN 4.3 2.9 - - - +
55A LEU* 2.8 47.6 + - - +
85A LEU* 5.2 0.6 - - - +
144A LEU 3.6 10.9 + - - +
145A GLU* 3.2 6.8 + - - +
147A TYR* 1.3 78.8 - - - +
149A LYS* 1.3 69.6 + - + +
151A GLY* 3.0 18.5 + - - -
152A GLN 3.7 9.2 - - - +
154A ILE* 3.6 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.5 40.6 - - + +
145A GLU* 2.8 45.2 + - + +
146A ALA 4.1 1.6 - - - +
148A GLN* 1.3 82.0 + - - +
150A THR* 1.3 60.4 + - - +
151A GLY 3.2 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.9 20.4 + - - +
7A LEU* 3.4 11.9 - - - +
10A TYR* 3.6 35.0 - - + -
146A ALA 2.6 24.4 + - - +
147A TYR* 2.7 15.8 + - - -
149A LYS* 1.3 77.4 - - - +
151A GLY* 1.3 60.9 + - - +
152A GLN* 3.5 19.1 + - - +
----------------------------------------------------------
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