Contacts of the helix formed by residues 122 - 136 (chain A) in PDB entry 1V40
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 TYR 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 3.1 34.1 + - + +
121A THR* 1.3 105.1 - - + +
123A ASN* 1.3 72.2 + - - +
124A ALA 3.4 0.9 - - - -
125A PRO* 3.1 10.6 - - - +
126A HIS* 3.1 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.6 17.3 - - + -
118A GLU* 3.4 9.0 + - - +
119A LEU* 3.0 46.9 + - - +
122A TYR* 1.3 78.1 - - - +
124A ALA* 1.3 65.2 + - - +
126A HIS* 3.1 19.2 + - - +
127A LEU* 3.1 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.7 21.3 - - + -
102A PHE* 6.0 0.2 - - + -
119A LEU 2.7 20.7 + - - +
120A LEU* 3.4 14.4 - - + +
123A ASN* 1.3 72.2 - - - +
125A PRO* 1.3 71.8 - - + +
127A LEU* 3.1 5.7 + - - +
128A MET* 2.9 29.2 + - + +
160A LEU* 5.7 2.0 - - + -
164A LYS* 4.9 0.7 - - + -
167A LEU* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU 3.3 12.8 - - - +
121A THR 3.4 17.0 - - - +
122A TYR* 3.1 15.5 - - - +
124A ALA* 1.3 95.2 - - + +
126A HIS* 1.3 58.4 + - + +
128A MET* 3.4 9.2 + - + +
129A GLN* 3.0 28.1 + - - +
164A LYS* 4.4 11.4 - - - -
167A LEU* 5.2 2.2 - - + +
171A HIS* 4.5 5.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 3.1 31.3 + - + +
123A ASN* 3.1 10.1 + - - +
125A PRO* 1.3 75.3 - - + +
127A LEU* 1.3 67.6 + - - +
129A GLN* 3.1 8.4 + - - +
130A ASP* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 3.9 28.5 - - + +
95A LEU* 4.6 10.8 - - + -
98A PHE* 3.6 44.6 - - + -
123A ASN 3.1 8.9 + - - +
124A ALA* 3.1 10.2 + - - +
126A HIS* 1.3 77.9 - - - +
128A MET* 1.3 68.3 + - + +
130A ASP* 3.1 7.8 + - + +
131A LEU* 2.8 44.3 + - + +
160A LEU* 5.9 0.2 - - + -
648D PHE* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 5.8 0.2 - - + -
98A PHE* 5.1 0.2 - - + -
124A ALA* 2.9 25.7 + - - +
125A PRO* 3.6 7.2 - - + +
127A LEU* 1.3 98.6 - - + +
129A GLN* 1.3 58.4 + - - +
131A LEU* 3.3 8.5 + - + -
132A ASP* 2.8 31.7 + - - +
153A TRP* 3.6 28.3 - - + -
160A LEU* 4.2 20.9 - - + -
167A LEU* 3.4 37.9 - - + +
168A LEU* 4.0 4.3 - - + -
171A HIS* 3.7 21.5 - - + +
174A LEU* 3.6 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO 3.0 14.4 + - - +
126A HIS* 3.1 12.3 + - - +
128A MET* 1.3 76.5 - - - +
130A ASP* 1.3 62.5 + - - +
132A ASP* 3.2 8.0 + - - +
133A THR* 2.8 54.3 + - - +
171A HIS* 3.7 19.7 + - - +
173A ARG* 6.1 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
126A HIS* 2.9 19.6 + - - +
127A LEU* 3.6 9.8 - - - +
129A GLN* 1.3 80.9 - - - +
131A LEU* 1.3 57.8 + - - +
133A THR* 3.2 7.0 + - - -
134A TYR* 2.8 30.0 + - - +
647D PRO 3.5 17.2 - - - +
648D PHE* 3.6 41.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
91A ILE* 4.8 16.6 - - + -
94A THR* 5.6 1.6 - - + -
95A LEU* 3.8 24.0 - - + -
127A LEU* 2.8 34.3 + - + +
128A MET* 3.7 8.5 - - + +
130A ASP* 1.3 73.3 - - - +
132A ASP* 1.3 58.3 + - - +
134A TYR* 3.0 7.2 + - + +
135A LEU* 2.8 31.2 + - - +
141A LEU* 4.9 12.0 - - + +
153A TRP* 3.5 35.2 - - + -
174A LEU* 4.2 14.0 - - + +
648D PHE* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET 2.8 18.6 + - - +
129A GLN* 3.5 7.7 + - - +
131A LEU* 1.3 76.1 - - - +
133A THR* 1.3 61.7 + - - +
135A LEU* 3.4 2.0 + - - +
136A GLY 3.1 18.2 + - - +
170A ASN 4.2 1.6 - - - +
171A HIS* 2.8 43.4 - - + +
172A PRO* 5.2 0.7 - - - +
173A ARG* 2.7 48.9 + - - +
174A LEU* 4.0 16.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
129A GLN* 2.8 36.6 + - - +
130A ASP* 3.6 7.4 - - - -
132A ASP* 1.3 76.9 - - - +
134A TYR* 1.3 64.2 + - - +
136A GLY* 3.4 12.2 + - - +
173A ARG* 4.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 3.7 26.3 + + - +
91A ILE* 3.4 33.1 - - + +
130A ASP 2.8 16.9 + - - +
131A LEU* 3.0 5.8 + - + +
133A THR* 1.3 78.9 - - - +
135A LEU* 1.3 51.1 + - - +
138A ARG* 2.6 36.1 + - - -
141A LEU* 3.5 32.1 - - + -
142A ILE* 4.1 1.4 - - - +
3002A GOL 3.5 17.9 + - - -
647D PRO* 4.9 9.0 - - + +
648D PHE* 3.9 25.8 - + + -
662D HIS* 4.7 7.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 2.8 15.6 + - - +
132A ASP 3.8 3.8 - - - +
134A TYR* 1.3 73.5 - - - +
136A GLY* 1.3 66.6 + - - +
138A ARG* 2.5 66.8 + - - +
139A GLU 4.5 0.9 - - - +
140A TRP* 3.5 31.2 - - - +
141A LEU* 3.9 14.1 - - + +
173A ARG* 3.7 32.5 - - + +
174A LEU* 3.9 18.6 - - + -
177A LEU* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASP 3.1 10.3 + - - -
133A THR* 3.4 10.0 + - - -
134A TYR 3.3 2.4 - - - -
135A LEU* 1.3 86.3 - - - +
137A GLY* 1.3 59.0 + - - -
138A ARG* 3.5 3.7 + - - +
173A ARG* 3.3 34.9 + - - +
----------------------------------------------------------
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