Contacts of the helix formed by residues 128 - 139 (chain A) in PDB entry 1ZVM
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 ILE 128 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 3.6 4.4 - - + -
126A SER 3.7 10.8 - - - +
127A ARG* 1.3 79.9 - - - +
129A LYS* 1.3 67.7 + - - +
130A ASP 3.4 2.5 - - - -
131A LEU* 3.3 17.5 + - + +
132A ALA* 3.3 12.6 + - - +
207A MET* 3.6 38.4 - - + +
208A LEU* 4.3 0.9 - - - +
209A ASP* 4.0 22.7 - - + +
243A ILE* 3.5 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 3.4 39.5 - - + -
127A ARG 3.8 0.4 - - - -
128A ILE* 1.3 76.7 - - - +
130A ASP* 1.3 67.7 + - - +
132A ALA* 3.1 1.8 + - - +
133A HIS* 2.9 62.9 + - + +
146A GLU* 4.8 0.7 - - - -
155A ASP* 2.9 24.7 + - - +
156A ASP* 2.7 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE 3.3 1.0 + - - -
129A LYS* 1.3 88.0 - - - +
131A LEU* 1.3 62.0 + - - +
133A HIS* 3.6 4.8 + - - +
134A GLN* 3.1 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.3 18.3 + - + +
129A LYS 3.3 0.4 - - - -
130A ASP* 1.3 76.9 - - - +
132A ALA* 1.3 67.1 + - - +
134A GLN* 3.2 6.2 + - - +
135A PHE* 2.9 23.4 + - - +
207A MET* 3.8 12.3 - - + -
243A ILE* 3.5 48.2 - - + -
281A PRO* 4.0 18.6 - - + +
284A PHE* 5.1 5.2 - - + -
285A LEU* 3.6 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.9 13.8 - - + +
125A TRP* 3.7 43.3 - - + -
128A ILE 3.3 5.5 + - - +
129A LYS 3.1 7.6 + - - +
131A LEU* 1.3 78.3 - - - +
133A HIS* 1.3 60.1 + - - +
135A PHE* 3.4 3.3 + - - +
136A THR* 3.2 31.4 + - - +
144A THR* 3.8 3.3 - - + +
207A MET* 3.6 12.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 4.0 5.2 - - - -
129A LYS* 2.9 49.5 + - + +
130A ASP* 4.1 5.4 - - - +
132A ALA* 1.3 77.7 - - - +
134A GLN* 1.3 64.2 + - + +
136A THR* 3.3 7.7 + - - -
137A GLN* 3.1 31.0 + - + +
144A THR* 3.4 17.4 + - - +
146A GLU* 2.8 44.3 + - + +
147A ASP* 5.1 3.1 + - - +
155A ASP* 3.8 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP* 3.1 36.6 + - + +
131A LEU* 3.2 9.9 + - - +
133A HIS* 1.3 74.1 - - + +
135A PHE* 1.3 65.8 + - - +
137A GLN* 3.3 15.8 + - - +
138A VAL* 3.3 20.1 + - + +
285A LEU* 3.8 29.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
123A LEU* 3.8 20.2 - - + -
131A LEU* 2.9 17.9 + - + +
132A ALA 3.5 4.5 - - - +
134A GLN* 1.3 77.3 - - - +
136A THR* 1.3 63.8 + - + +
138A VAL* 3.2 4.7 + - - +
139A GLN* 2.8 47.8 + - + +
142A MET* 3.8 27.6 - - + -
207A MET* 4.2 10.8 - - + -
241A TRP* 3.7 22.0 - + - -
284A PHE* 3.6 37.0 - + + -
285A LEU* 3.8 11.8 - - + +
288A VAL* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.3 2.7 - - + -
132A ALA 3.2 6.5 + - - +
133A HIS* 3.3 14.4 + - - -
134A GLN 3.4 0.2 - - - -
135A PHE* 1.3 86.4 - - + +
137A GLN* 1.3 66.6 + - - +
138A VAL 3.1 0.2 - - - -
139A GLN 3.2 21.6 - - - +
140A ARG* 3.3 10.2 - - - +
142A MET* 3.5 28.2 - - + +
143A PHE 4.2 0.9 - - - -
144A THR* 3.6 20.6 - - + +
147A ASP* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A HIS* 3.1 26.9 + - + +
134A GLN* 3.6 9.6 - - - +
135A PHE 3.2 0.4 - - - -
136A THR* 1.3 79.5 + - - +
138A VAL* 1.3 62.5 + - + +
140A ARG* 3.5 30.4 + - - +
147A ASP* 4.5 12.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN 3.5 12.6 - - - +
135A PHE* 3.2 7.7 + - - +
137A GLN* 1.3 82.2 - - + +
139A GLN* 1.3 58.6 + - - +
140A ARG* 3.1 11.1 + - - +
285A LEU* 4.4 11.9 - - + +
288A VAL* 3.5 17.0 - - + +
289A LYS* 3.5 59.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 2.8 46.2 + - + +
136A THR* 3.2 11.0 - - - +
138A VAL* 1.3 69.0 - - - +
140A ARG* 1.3 58.4 + - - +
141A ASP* 2.8 29.8 + - - +
142A MET* 3.0 32.4 + - + +
288A VAL* 3.4 24.1 - - + +
----------------------------------------------------------
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