Contacts of the helix formed by residues 114 - 126 (chain C) in PDB entry 1IVH
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 GLU 114 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLN* 3.7 12.5 + - - +
69C TYR* 3.2 17.3 + - - -
113C ASN* 1.3 74.3 - - - +
115C ALA* 1.3 56.6 + - - +
117C LYS* 3.0 30.5 + - - +
118C GLU* 3.1 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ASN* 3.0 11.6 - - - +
114C GLU* 1.3 75.7 - - - +
116C GLN* 1.3 62.1 - - + +
118C GLU* 3.1 6.3 + - - +
119C LYS* 2.8 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 4.8 4.4 - - + +
111C ASN 4.4 1.2 - - - +
112C GLY* 3.3 12.0 - - - -
113C ASN* 2.9 43.8 + - - +
115C ALA* 1.3 76.7 - - + +
117C LYS* 1.3 58.2 + - - +
119C LYS* 3.2 1.3 + - - -
120C TYR* 2.9 48.1 + - + +
197C ILE* 3.7 28.9 - - + +
234C ALA 3.1 23.9 + - - +
235C ASN* 3.9 1.2 - - - +
236C ILE 2.9 29.1 + - - +
237C LEU* 4.2 2.9 - - - +
238C GLY 4.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PRO* 5.6 0.7 - - + -
69C TYR* 3.5 30.7 + - + +
108C LEU* 3.6 24.5 - - + +
109C VAL* 4.1 15.4 + - + +
112C GLY* 3.2 23.2 + - - +
113C ASN* 3.0 18.0 + - - +
114C GLU* 3.0 23.2 + - - +
116C GLN* 1.3 77.9 - - - +
118C GLU* 1.3 58.3 + - - +
121C LEU* 2.9 59.6 + - + +
122C PRO* 3.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLN* 4.1 11.1 - - - +
69C TYR* 3.7 24.4 - - + +
114C GLU* 3.1 28.5 + - + +
115C ALA* 3.6 4.9 - - - +
117C LYS* 1.3 77.6 - - - +
119C LYS* 1.3 58.2 + - - +
122C PRO* 3.2 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ALA 2.8 17.1 + - - +
116C GLN* 3.8 3.4 - - - +
118C GLU* 1.3 79.5 - - - +
120C TYR* 1.3 84.9 + - + +
122C PRO* 4.5 4.6 - - - +
123C LYS* 5.5 4.3 + - - +
129C TYR* 5.2 5.9 - - - -
199C GLU* 3.5 28.6 + - - -
235C ASN* 5.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 4.1 14.4 - - + -
116C GLN* 2.9 40.0 + - + +
119C LYS* 1.3 102.5 - - + +
121C LEU* 1.3 65.0 + - - +
122C PRO 3.2 3.6 - - - -
123C LYS* 3.3 11.1 + - - +
124C LEU* 3.1 28.7 - - + +
129C TYR* 4.9 11.2 - + - -
175C VAL* 3.8 17.7 - - + -
197C ILE* 3.6 31.1 - - + +
199C GLU* 2.7 36.9 + - + -
235C ASN* 2.7 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PRO* 4.7 0.7 - - + -
69C TYR* 3.6 25.4 - - + -
105C ILE* 4.2 17.3 - - + +
108C LEU* 3.8 30.5 - - + -
109C VAL* 3.7 27.1 - - + -
117C LYS* 2.9 52.5 + - + +
120C TYR* 1.3 75.8 - - - +
122C PRO* 1.3 57.6 - - + +
124C LEU* 3.1 3.6 + - - +
125C ILE* 2.8 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TYR* 3.9 24.6 - - + +
117C LYS 3.2 12.8 - - - +
118C GLU* 3.2 22.9 - - - +
119C LYS 4.5 4.3 - - - +
120C TYR 4.2 2.0 - - - +
121C LEU* 1.3 90.0 - - + +
123C LYS* 1.3 62.6 + - + +
125C ILE* 3.4 2.1 + - - +
126C SER* 3.0 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS 5.5 4.5 - - - +
120C TYR 3.3 4.8 + - - +
122C PRO* 1.3 80.4 - - + +
124C LEU* 1.3 63.1 + - - +
126C SER* 3.5 6.3 - - - -
127C GLY 3.2 1.7 + - - -
128C GLU* 3.0 42.6 + - + +
129C TYR* 3.0 68.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.0 1.6 - - - +
100C HIS* 2.7 51.2 + - + +
104C CYS* 4.4 2.9 - - - -
105C ILE* 3.6 23.1 - - + +
108C LEU* 4.7 8.7 - - + -
120C TYR* 3.1 35.4 + - + +
121C LEU* 3.1 10.5 + - + +
123C LYS* 1.3 78.0 - - - +
125C ILE* 1.3 62.2 + - - +
126C SER 3.6 0.2 + - - -
127C GLY 3.7 4.5 + - - -
129C TYR* 3.8 16.4 - - + +
131C GLY* 3.7 13.5 - - - +
175C VAL* 3.3 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLY* 3.5 11.6 - - - +
59C GLY* 5.7 3.5 - - - +
61C LEU* 3.5 16.5 - - - +
62C GLY* 3.9 24.8 + - - +
65C ALA* 3.8 20.9 - - + -
69C TYR* 3.3 33.4 - - + +
70C GLY* 3.4 26.5 - - - +
71C GLY* 4.0 1.6 - - - +
105C ILE* 4.1 11.2 - - + -
121C LEU* 2.8 35.8 + - + +
122C PRO 3.8 4.0 - - - +
124C LEU* 1.3 79.2 - - - +
126C SER* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C TRP 3.7 3.5 - - - +
53C LYS* 3.7 12.9 - - - +
56C GLY* 3.3 22.2 - - - -
122C PRO 3.0 14.5 + - - -
123C LYS* 3.2 12.6 + - - -
125C ILE* 1.3 76.8 - - - +
127C GLY* 1.3 59.5 + - - +
128C GLU* 3.1 30.8 + - - +
----------------------------------------------------------
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