Contacts of the helix formed by residues 134 - 148 (chain A) in PDB entry 1YSD
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 134 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 5.3 0.3 - - - +
15A MET* 3.8 12.9 - - + +
109A GLY* 2.7 20.7 + - - +
110A GLU* 4.4 0.9 - - - +
132A VAL* 3.4 14.0 - - + +
133A ASP* 1.3 70.7 - - - +
135A GLU* 1.3 63.3 + - - +
136A ARG* 2.8 70.0 + - - +
137A CYS* 3.2 21.6 + - - +
138A LYS* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 3.4 12.4 + - - +
134A ASP* 1.3 69.7 + - - +
136A ARG* 1.3 61.0 + - + +
138A LYS* 2.9 41.4 + - - +
139A LYS* 2.9 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 4.0 8.1 + - - -
15A MET* 4.7 3.0 - - - +
16A ASP* 3.0 33.7 + - - +
19A TYR* 3.6 52.6 + - + +
134A ASP* 2.8 33.6 + - - +
135A GLU* 1.3 77.0 - - + +
137A CYS* 1.3 61.1 + - - +
139A LYS* 4.0 6.6 - - - +
140A LEU* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MET* 4.4 7.2 - - - -
19A TYR* 4.0 21.3 - - - -
32A PRO 5.8 0.2 - - - +
87A THR* 3.6 53.2 - - - +
109A GLY* 4.5 0.9 - - - -
110A GLU* 4.3 4.7 - - + -
134A ASP* 3.2 30.3 + - + +
136A ARG* 1.3 77.5 - - - +
138A LYS* 1.3 65.7 + - - +
140A LEU* 3.3 4.3 + - - +
141A MET* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 3.5 22.4 - - + +
112A VAL* 3.7 31.6 - - + +
113A ASN* 3.1 18.8 - - - +
133A ASP* 2.8 33.0 + - - -
134A ASP 3.1 11.2 + - - +
135A GLU* 2.9 39.1 + - - +
136A ARG 3.4 0.2 - - - -
137A CYS* 1.3 79.5 - - - +
139A LYS* 1.3 57.6 + - + +
142A LYS* 3.0 30.3 + - + +
----------------------------------------------------------
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 GLU* 2.9 42.9 + - - +
136A ARG* 4.0 5.6 - - - +
138A LYS* 1.3 77.9 - - + +
140A LEU* 1.3 62.2 + - - +
142A LYS* 3.4 5.4 + - - +
143A GLN* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 4.1 9.2 - - + +
22A ALA* 3.9 10.5 - - + -
23A LEU* 3.6 43.5 - - + +
26A TYR* 3.8 35.8 - - + -
32A PRO* 3.7 23.2 - - + +
136A ARG 3.2 16.4 + - - +
137A CYS* 3.3 5.4 + - - +
139A LYS* 1.3 79.5 - - - +
141A MET* 1.3 60.9 + - - +
143A GLN* 3.4 8.9 + - + +
144A PHE* 3.3 19.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
31A VAL* 4.3 4.5 - - + -
32A PRO* 3.9 19.0 + - - +
33A ILE* 3.8 22.7 - - - -
88A LEU* 4.0 13.0 - - + -
110A GLU* 3.7 4.5 - - - +
113A ASN* 3.6 27.4 - - + +
137A CYS 3.0 16.8 + - - +
140A LEU* 1.3 74.6 - - - +
142A LYS* 1.3 65.8 + - - +
144A PHE* 3.3 15.3 + - + +
145A ILE* 3.0 42.0 + - + +
152A TRP* 3.4 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 3.6 23.5 + - - +
138A LYS* 3.0 20.7 + - + +
139A LYS* 3.7 6.5 - - - +
140A LEU 3.3 0.2 - - - -
141A MET* 1.3 75.6 - - - +
143A GLN* 1.3 58.2 + - - +
145A ILE* 3.3 9.0 + - + +
146A ASP* 2.6 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.6 23.2 + - + +
139A LYS 3.0 17.5 + - - +
140A LEU* 3.6 9.2 - - + +
141A MET 3.2 0.2 - - - -
142A LYS* 1.3 77.3 - - - +
144A PHE* 1.3 63.0 + - - +
146A ASP* 3.2 15.5 + - - +
147A GLU* 3.1 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 4.2 9.4 - + + -
30A GLY 3.6 13.7 - - - -
31A VAL* 4.0 22.7 - - + -
32A PRO* 3.4 35.4 - - + -
140A LEU 3.3 4.5 + - - +
141A MET* 3.3 15.7 + - + +
143A GLN* 1.3 79.4 - - - +
145A ILE* 1.3 61.6 + - - +
147A GLU* 3.4 16.5 - - - +
148A ARG* 2.8 66.3 + - + -
151A ASP* 3.8 20.6 - - + -
152A TRP* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 3.9 36.3 - - + +
141A MET* 3.0 35.0 + - + +
142A LYS* 3.7 9.6 - - + +
144A PHE* 1.3 77.0 - - - +
146A ASP* 1.3 66.4 + - - +
149A PRO* 3.1 33.6 - - + +
152A TRP* 3.7 39.7 - - + +
153A PHE* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 2.6 58.4 + - - +
143A GLN* 3.4 18.6 + - - +
144A PHE 3.2 0.2 - - - -
145A ILE* 1.3 80.7 - - - +
147A GLU* 1.3 59.0 + - + +
149A PRO* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 2.6 41.0 + - - -
143A GLN* 3.1 36.2 + - - +
144A PHE* 3.4 12.0 - - - +
146A ASP* 1.3 79.2 - - + +
148A ARG* 1.3 77.9 + - + +
149A PRO* 3.4 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 6.0 1.2 - - - -
29A GLY* 2.9 35.4 + - - -
54A PHE* 3.4 27.7 - - - -
144A PHE* 2.8 48.1 + - + +
145A ILE 4.4 0.2 - - - -
147A GLU* 1.3 93.3 + - + +
149A PRO* 1.3 65.0 - - - +
150A GLN* 3.3 2.5 - - - -
151A ASP* 2.6 45.4 + - + +
152A TRP* 3.2 10.4 + - - +
----------------------------------------------------------
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