Contacts of the helix formed by residues 131 - 148 (chain A) in PDB entry 4R1Z
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 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 5.8 0.7 - - - +
129A ASP* 3.3 10.4 + - - -
130A TYR* 1.3 83.5 - - - +
132A SER* 1.3 60.5 + - - +
133A THR* 3.5 12.2 + - - -
134A TRP* 3.0 22.2 + - - +
135A LYS* 2.8 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 1.3 73.3 - - - +
133A THR* 1.3 59.2 + - - +
135A LYS* 3.6 13.7 - - - +
136A PHE* 2.9 31.2 + - - +
295A ASP 4.2 13.0 + - - -
296A VAL* 3.8 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.6 9.2 + - - -
132A SER* 1.3 75.4 + - - +
134A TRP* 1.3 67.7 + - - +
136A PHE 3.1 1.6 + - - -
137A HIS* 2.9 52.1 + - + +
295A ASP 4.3 4.2 + - - -
296A VAL* 4.0 10.9 - - - +
297A GLY* 3.4 34.9 + - - +
302A HIS* 4.2 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP 5.6 1.1 - - - -
125A ILE* 3.6 31.5 - - + +
128A ALA* 3.9 12.1 - - + +
129A ASP 3.6 8.7 - - - +
130A TYR* 3.4 35.7 - + - -
131A SER* 3.0 26.1 + - - +
133A THR* 1.3 80.0 - - - +
135A LYS* 1.3 93.9 + - + +
137A HIS* 3.4 4.0 + - - +
138A ARG* 3.1 46.9 + - - +
450A VAL* 3.4 37.5 - - + -
451A ARG* 3.4 19.0 - - - +
600A HEM 2.9 21.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 3.7 36.0 + - - -
131A SER 2.8 21.4 + - - +
132A SER* 3.6 14.2 - - - +
134A TRP* 1.3 87.6 - - + +
136A PHE* 1.3 59.6 + - - +
138A ARG* 3.3 7.0 + - - +
139A LYS* 2.9 28.7 + - - +
157B LYS* 6.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER 2.9 22.1 + - - +
133A THR 3.6 2.9 - - - +
135A LYS* 1.3 75.2 - - - +
137A HIS* 1.3 67.1 + + - +
139A LYS* 3.2 10.0 + - + +
140A MET* 3.0 62.0 + - + +
282A ALA* 4.5 6.7 - - + -
296A VAL* 3.4 31.4 - - + -
298A LEU* 4.0 26.2 - - + -
150B GLU* 4.1 6.5 - - + -
151B GLY* 3.5 38.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LYS 5.7 0.9 - - - -
124A ASP 5.7 2.5 - - - +
125A ILE* 3.9 16.6 - - + -
133A THR* 2.9 40.8 + - + +
134A TRP* 4.1 1.1 - - - +
136A PHE* 1.3 76.9 - + - +
138A ARG* 1.3 67.4 + - - +
140A MET* 3.0 17.4 + - - +
141A VAL* 3.2 17.8 + - - +
279A LEU* 4.2 13.9 - - + +
296A VAL* 4.5 0.2 - - + -
297A GLY 3.0 29.1 + - - -
298A LEU* 3.7 19.0 - - + +
302A HIS* 3.6 18.6 + + + +
303A VAL 4.6 0.2 + - - -
306A THR* 2.9 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.0 9.8 - - + +
134A TRP* 3.1 38.8 + - - +
135A LYS* 3.3 10.1 - - - +
137A HIS* 1.3 79.1 - - - +
139A LYS* 1.3 60.7 + - - +
141A VAL* 3.4 3.1 + - - +
142A HIS* 3.3 20.7 + - - +
450A VAL 3.8 10.4 + - - -
451A ARG 3.9 0.6 - - - -
452A VAL* 2.2 52.1 + - - +
453A CYS 3.9 1.4 + - - -
454A LEU* 3.6 43.5 - - + +
600A HEM 2.7 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LYS 2.9 13.5 + - - +
136A PHE* 3.3 12.8 - - + +
137A HIS 3.1 0.2 - - - -
138A ARG* 1.3 77.7 - - - +
140A MET* 1.3 70.8 + - + +
141A VAL 3.1 0.7 + - - -
142A HIS* 3.2 14.7 + - + +
143A GLY* 3.2 10.6 + - - -
146B CYS 4.5 10.9 - - - +
147B MET* 4.6 10.2 - - + +
148B PHE 4.3 1.1 - - - -
149B GLY* 3.2 43.0 - - - +
150B GLU* 4.0 2.7 - - - +
151B GLY* 3.6 21.5 - - - +
152B SER 3.6 6.5 - - - +
153B VAL 4.1 1.4 + - - -
154B SER* 3.4 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.0 56.9 + - + +
137A HIS* 3.0 9.2 + - - +
139A LYS* 1.3 79.0 - - + +
141A VAL* 1.3 58.9 + - + +
143A GLY* 3.4 0.9 + - - -
144A ALA* 2.9 31.0 + - - +
275A LEU* 4.0 6.0 - - + +
278A ALA* 4.1 17.8 - - - +
279A LEU* 3.8 24.7 - - + -
282A ALA* 4.0 18.6 - - + -
147B MET* 6.1 4.7 - - + -
150B GLU* 4.0 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.2 2.5 - - + -
137A HIS 3.2 14.1 + - - +
138A ARG 3.8 5.6 - - - +
139A LYS 3.1 1.0 - - - -
140A MET* 1.3 74.7 - - + +
142A HIS* 1.3 66.2 + - - +
144A ALA* 3.9 0.9 - - - +
145A LEU* 3.1 24.3 + - + +
195A LEU* 5.5 3.0 - - + +
275A LEU* 3.9 19.7 - - + -
306A THR* 4.0 24.5 - - + -
310A ILE* 3.7 33.9 - - + -
454A LEU* 3.9 22.7 - - + +
600A HEM 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG 3.3 10.3 + - - +
139A LYS* 3.2 10.8 + - - +
141A VAL* 1.3 81.7 - - - +
143A GLY* 1.3 57.0 + - - +
145A LEU* 3.3 12.8 + - + +
146A CYS* 2.9 33.7 + - - -
454A LEU* 4.8 15.9 - - + +
457A ALA* 5.8 7.4 - - + +
146B CYS* 3.7 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS 3.2 12.8 + - - -
140A MET* 3.9 1.8 - - - -
142A HIS* 1.3 74.7 + - - +
144A ALA* 1.3 64.4 + - - +
146A CYS* 3.1 7.6 + - - +
147A MET* 2.9 20.6 + - - +
146B CYS* 4.2 9.8 - - - -
147B MET* 3.2 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A MET 2.9 18.6 + - - +
141A VAL 3.9 2.9 - - - +
143A GLY* 1.3 73.9 - - - +
145A LEU* 1.3 58.0 + - - +
148A PHE* 2.8 34.5 + - - +
195A LEU* 5.2 3.6 - - + +
272A GLN* 4.3 14.6 + - - +
274A ASP 5.9 0.3 - - - -
275A LEU* 3.5 42.6 + - + +
278A ALA* 4.3 7.0 - - + -
147B MET* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 3.1 18.2 + - + +
142A HIS* 3.5 12.1 - - + +
143A GLY 3.1 0.2 - - - -
144A ALA* 1.3 78.8 - - - +
146A CYS* 1.3 68.9 + - - +
147A MET 3.3 0.3 + - - -
148A PHE* 3.6 12.8 - - - +
155A ILE* 3.8 30.4 - - + +
195A LEU* 4.0 31.1 - - + +
454A LEU 5.5 5.6 - - - +
455A GLY* 6.1 0.7 - - - -
457A ALA* 4.6 17.0 - - + -
458A LEU* 4.3 31.4 - - + +
461A MET* 5.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A HIS* 2.9 25.8 + - - -
143A GLY 3.1 7.6 + - - +
145A LEU* 1.3 79.0 - - - +
147A MET* 1.3 61.2 + - - +
148A PHE 4.2 3.1 - - - +
154A SER* 4.9 3.5 + - - -
139B LYS* 4.5 10.0 - - - +
142B HIS* 4.3 27.7 + - + -
143B GLY* 4.2 10.1 - - - -
146B CYS* 2.1 51.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY 2.9 4.5 + - - +
144A ALA 4.6 0.4 - - - +
146A CYS* 1.3 76.5 - - - +
148A PHE* 1.3 62.0 + - - +
149A GLY* 2.8 16.3 - - - -
150A GLU* 3.5 9.7 - - - +
272A GLN* 5.2 7.4 - - - +
139B LYS* 3.9 9.6 - - + +
140B MET* 3.3 43.5 - - + +
143B GLY* 3.4 15.5 - - - -
144B ALA* 3.1 34.3 - - + +
147B MET* 3.4 34.8 - - + +
272B GLN* 5.0 0.9 - - - +
278B ALA* 4.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA 2.8 19.3 + - - +
145A LEU 3.6 10.4 - - - +
146A CYS 4.2 1.6 - - - +
147A MET* 1.3 75.2 - - - +
149A GLY* 1.3 64.1 + - - +
153A VAL* 4.8 5.8 - - + -
154A SER* 3.6 17.0 + - - -
155A ILE* 3.8 10.3 + - + +
158A ILE* 3.0 36.8 - - + -
194A ALA* 2.9 32.3 - - + -
195A LEU* 3.9 30.3 - - + +
198A ASN* 3.9 13.2 - - - -
272A GLN* 5.5 3.7 - - - +
273A ARG 3.4 27.4 - - - -
274A ASP* 4.2 4.7 - - - -
275A LEU 6.2 0.2 - - - +
139B LYS* 4.1 1.1 - - - -
----------------------------------------------------------
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