Contacts of the helix formed by residues 97 - 108 (chain B) in PDB entry 1V8C
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 PRO 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA 3.3 11.9 - - - +
96B PHE* 1.3 89.9 - - + +
98B PRO* 1.3 74.1 - - + +
99B TRP* 3.4 30.5 - - + +
100B LEU* 3.0 36.9 + - + +
101B LEU* 3.1 12.1 + - - +
143B LEU* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE 3.5 2.7 - - - +
97B PRO* 1.3 83.3 - - + +
99B TRP* 1.3 59.1 + - + +
101B LEU* 3.2 4.0 + - + +
102B GLU* 2.8 45.4 + - - +
127B PHE* 4.5 11.9 - - + -
129B GLU* 3.3 31.2 - - + +
143B LEU* 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO* 3.4 27.7 - - + +
98B PRO* 1.3 80.1 - - + +
100B LEU* 1.3 77.6 + - + +
102B GLU* 3.5 15.6 + - - +
103B ARG* 3.0 63.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 4.1 15.7 - - + -
97B PRO* 3.0 33.0 + - + +
99B TRP* 1.3 95.5 - - + +
101B LEU* 1.3 66.2 + - - +
103B ARG* 3.0 34.0 + - - +
104B TYR* 3.0 49.6 + - + -
162B ALA 5.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 3.8 32.6 - - + -
97B PRO 3.1 10.2 + - - +
98B PRO* 3.2 8.0 + - + +
100B LEU* 1.3 76.2 - - - +
102B GLU* 1.3 59.3 + - - +
104B TYR* 3.1 8.6 + - + +
105B LEU* 2.9 55.9 + - + +
108B TRP* 5.4 0.7 - - + -
125B VAL* 5.1 0.7 - - + -
127B PHE* 3.7 37.7 - - + -
143B LEU* 3.9 16.2 - - + -
145B VAL* 4.1 13.5 - - + -
159B ILE* 4.1 18.6 - - + -
162B ALA* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 2.8 31.3 + - - +
99B TRP* 3.6 13.8 - - - +
101B LEU* 1.3 77.4 - - - +
103B ARG* 1.3 62.7 + - - +
105B LEU* 3.3 7.8 + - - +
106B GLU* 3.0 35.6 + - - +
112B ARG* 6.0 1.2 + - - -
115B GLU* 4.9 8.5 - - - +
116B GLY 5.5 0.2 + - - -
118B TYR* 3.6 26.2 + - + +
127B PHE* 3.7 32.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 3.0 41.4 + - + +
100B LEU* 3.0 28.9 + - + +
102B GLU* 1.3 75.8 - - - +
104B TYR* 1.3 58.1 + - + +
106B GLU* 3.7 13.5 + - - +
107B GLU* 3.0 33.1 + - + +
47D GLU* 5.0 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 4.8 2.5 - + - -
100B LEU* 3.0 49.7 + - + +
101B LEU* 3.1 11.9 + - + +
103B ARG* 1.3 75.2 - - - +
105B LEU* 1.3 66.9 + - - +
107B GLU* 3.1 14.1 + - - +
108B TRP* 2.9 57.8 + + + -
161B PHE* 5.9 2.4 - + - -
162B ALA* 3.8 38.5 + - + -
69D SER* 3.6 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 2.9 36.2 + - + +
102B GLU* 3.3 6.0 + - - +
104B TYR* 1.3 76.4 - - - +
106B GLU* 1.3 53.7 + - - +
108B TRP* 3.3 34.0 + - + +
109B GLY 3.5 0.2 + - - -
110B GLY* 2.7 34.8 + - - -
118B TYR* 3.7 43.3 - - + -
120B LEU* 4.0 20.9 - - + +
125B VAL* 4.3 13.2 - - + -
127B PHE* 3.9 17.0 - - + -
159B ILE* 4.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLU* 3.0 22.6 + - - +
103B ARG* 3.7 13.4 + - - +
105B LEU* 1.3 72.3 - - - +
107B GLU* 1.3 61.2 + - - +
108B TRP 3.0 1.8 - - - -
109B GLY* 2.9 19.9 + - - -
110B GLY 4.0 12.7 - - - +
112B ARG* 5.8 1.6 - - - +
118B TYR* 4.1 26.5 + - + -
47D GLU* 3.9 39.0 - - - +
48D GLY 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 3.0 25.1 + - + +
104B TYR* 3.4 15.1 - - - +
106B GLU* 1.3 76.4 - - - +
108B TRP* 1.3 60.7 + - + +
109B GLY 3.1 2.8 + - - -
1003B CL 4.2 0.2 - - - +
26D GLY* 5.4 2.4 - - - -
30D GLU* 5.9 3.6 - - - +
47D GLU* 3.4 21.1 + - + +
48D GLY* 3.6 1.9 - - - -
68D LEU* 3.4 50.0 - - + +
69D SER* 3.1 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 5.4 1.3 - - + -
104B TYR* 2.9 45.4 + + + +
105B LEU* 3.6 24.7 - - + +
106B GLU 3.0 0.8 - - - -
107B GLU* 1.3 84.3 - - + +
109B GLY* 1.3 59.0 + - - +
110B GLY 3.3 1.0 + - - -
120B LEU* 4.1 8.0 - - + +
121B PRO* 4.7 6.2 - - - +
155B TRP* 3.7 28.7 - + + -
158B ARG* 3.3 67.1 + - + +
159B ILE* 3.9 24.0 - - + -
161B PHE* 5.7 0.9 - + - -
162B ALA* 3.9 11.9 - - + -
1003B CL 3.8 13.7 - - + -
48D GLY* 4.8 1.8 - - - -
49D LEU 5.6 0.2 - - - -
66D GLN 4.5 0.9 - - - -
68D LEU 4.8 0.2 - - - -
69D SER* 2.9 30.3 + - - -
----------------------------------------------------------
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