Contacts of the helix formed by residues 130 - 140 (chain B) in PDB entry 5VZ4
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 130 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TRP* 1.3 69.9 - - - +
131B CYS* 1.3 61.7 - - - +
132B LEU* 3.3 13.3 + - - +
133B GLU* 3.3 34.0 + - - +
134B VAL* 3.1 25.3 + - - +
189B CYS* 4.2 0.7 - - - -
190B ASP 3.6 7.4 - - - -
195B ASP* 4.8 3.6 + - - -
198B CYS* 3.1 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TRP 3.4 2.0 + - - -
130B SER* 1.3 71.3 + - - +
132B LEU* 1.3 57.0 + - - +
134B VAL* 3.8 0.6 - - - +
135B ALA* 2.9 30.3 + - - +
189B CYS* 2.1 64.6 - - - -
190B ASP* 3.5 8.5 + - - -
191B CYS* 3.7 14.1 - - - -
198B CYS* 3.4 10.5 - - - +
201B SER* 3.8 4.5 - - - -
202B LYS* 3.9 28.3 - - - +
205B LEU* 3.7 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.0 25.1 - - + -
89A ILE* 4.9 7.0 - - + -
96A VAL* 4.6 13.5 - - + -
130B SER* 3.2 12.3 + - - +
131B CYS* 1.3 76.5 - - - +
133B GLU* 1.3 54.7 + - + +
135B ALA* 3.1 4.2 + - - +
136B GLU* 2.8 49.3 + - + +
195B ASP* 5.5 3.4 - - - +
197B PRO* 4.1 23.3 - - + +
198B CYS* 3.8 11.9 - - + +
201B SER* 3.6 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TRP* 5.3 0.5 - - - -
130B SER* 3.3 32.2 + - - +
132B LEU* 1.3 77.8 - - + +
134B VAL* 1.3 61.4 + - + +
136B GLU* 3.4 17.9 + - - +
137B ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TRP* 4.2 12.3 - - + -
130B SER 3.1 17.0 + - - +
131B CYS* 3.8 4.5 - - - +
133B GLU* 1.3 72.9 - - + +
135B ALA* 1.3 60.9 + - - +
137B ALA* 3.3 6.4 + - + +
138B CYS* 2.8 30.3 + - + +
182B ILE* 5.0 3.1 - - + +
185B MET* 3.7 35.4 - - + +
186B LEU* 3.5 46.0 - - + +
189B CYS* 4.1 6.5 - - + -
205B LEU* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.7 15.9 - - + -
98A LEU* 4.6 9.2 - - + -
131B CYS 2.9 19.6 + - - +
132B LEU* 3.3 7.0 - - - +
134B VAL* 1.3 76.5 - - - +
136B GLU* 1.3 52.0 + - - +
138B CYS* 3.7 4.5 - - - +
139B VAL* 2.8 39.9 + - - +
148B LEU* 5.9 0.2 - - - -
201B SER* 4.2 12.3 - - - +
205B LEU* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.3 46.5 - - + +
35A SER* 3.1 19.0 + - - +
37A ARG* 5.3 9.6 + - - +
89A ILE* 3.9 8.3 - - + -
132B LEU* 2.8 26.7 + - - +
133B GLU* 3.6 25.9 - - - +
134B VAL 3.3 0.2 - - - -
135B ALA* 1.3 73.0 - - - +
137B ALA* 1.3 56.1 + - - +
140B GLY* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU 3.0 16.6 + - - +
134B VAL* 3.7 7.2 - - + +
136B GLU* 1.3 72.3 - - - +
138B CYS* 1.3 66.4 + - - +
140B GLY* 3.5 2.2 + - - -
141B ASP* 3.4 21.1 + - - +
182B ILE* 6.2 2.0 - - + -
185B MET* 6.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL 2.8 21.4 + - - +
135B ALA* 3.8 3.8 - - - +
137B ALA* 1.3 72.7 - - - +
139B VAL* 1.3 62.9 + - - +
141B ASP* 3.2 9.9 + - - -
144B CYS* 2.1 59.6 - - - +
145B ASN 3.2 18.9 + - - -
148B LEU* 3.9 22.2 - - + -
174B PHE* 4.8 1.1 - - - -
182B ILE* 5.0 5.3 - - + +
186B LEU* 4.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.6 32.1 - - - +
36A PRO* 3.7 9.7 - - - +
87A VAL* 3.5 42.8 - - + +
89A ILE* 3.8 18.6 - - + -
98A LEU* 5.1 1.8 - - + -
135B ALA* 2.8 22.1 + - - +
138B CYS* 1.3 76.3 - - - +
140B GLY* 1.3 59.8 + - - +
141B ASP 3.4 1.6 + - - +
145B ASN* 2.8 29.9 + - - +
148B LEU* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.8 2.4 + - - -
36A PRO* 3.9 18.3 - - - +
37A ARG 5.4 0.9 - - - -
38A GLU 5.1 2.9 - - - +
136B GLU 2.9 18.6 + - - -
137B ALA* 3.8 4.0 - - - -
138B CYS 3.2 0.4 - - - -
139B VAL* 1.3 76.5 - - - +
141B ASP* 1.3 56.1 + - - +
142B VAL* 4.2 0.7 + - - +
----------------------------------------------------------
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