Contacts of the helix formed by residues 89 - 103 (chain I) in PDB entry 1V8P
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 THR 89 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I LEU* 1.3 77.9 - - - +
90I PHE* 1.3 64.9 + - - +
91I TYR* 3.2 12.6 + - - +
92I ASP* 3.0 38.2 + - - +
93I ALA* 2.9 20.1 + - - +
41J ASN* 4.2 4.5 - - - -
44J TRP* 3.7 29.2 - - + -
48K ARG* 6.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I LEU* 3.7 26.0 - - + -
79I VAL* 3.4 27.7 - - + +
80I LEU* 3.7 28.0 - - + -
83I ALA* 4.3 9.0 - - + -
88I LEU 3.8 0.6 + - - -
89I THR* 1.3 73.7 - - - +
91I TYR* 1.3 63.4 + + - +
93I ALA* 4.3 0.2 - - - -
94I SER* 2.8 41.4 + - - -
36J ILE* 4.3 3.1 - - + -
37J TYR* 3.6 35.2 - + + -
40J GLY* 3.3 34.1 - - - +
41J ASN* 3.3 25.8 - - - +
44J TRP* 3.9 9.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I LEU* 3.9 25.5 - - + +
38I GLU* 3.8 18.2 - - + +
89I THR* 3.5 9.6 - - - +
90I PHE* 1.3 77.6 - + - +
92I ASP* 1.3 59.0 + - - +
94I SER* 2.8 33.1 + - - -
95I TYR* 3.6 10.2 + - - -
34J LEU* 5.1 3.4 - - + +
37J TYR* 3.6 31.2 - - + -
38J GLU* 3.6 25.3 - - - +
41J ASN* 3.5 33.4 + - + +
91J TYR* 5.6 11.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I GLU* 5.6 0.7 - - - +
88I LEU* 4.2 12.0 - - + +
89I THR* 3.0 39.3 + - - +
91I TYR* 1.3 76.3 - - - +
93I ALA* 1.3 62.7 + - - +
95I TYR* 3.0 21.7 + - - +
96I ALA 3.3 8.7 + - - -
110I ASP* 4.0 14.9 - - - +
112I GLU* 5.7 1.2 - - - +
113I LEU* 3.5 39.3 - - + +
48K ARG* 4.7 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I VAL* 3.5 24.7 - - - +
82I VAL* 4.0 9.2 - - + +
83I ALA* 3.6 21.8 - - + +
88I LEU* 4.0 13.2 - - + +
89I THR 2.9 18.1 + - - +
90I PHE 3.7 4.0 - - - +
92I ASP* 1.3 76.8 - - - +
94I SER* 1.3 60.6 + - - +
96I ALA* 4.0 1.7 - - - +
97I TYR* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I LEU* 4.1 10.1 - - - -
34I LEU* 4.6 2.2 - - - -
74I PRO* 4.9 0.9 - - - -
79I VAL* 3.4 19.9 - - - +
90I PHE* 2.8 20.9 + - - -
91I TYR* 2.8 13.7 + - - -
93I ALA* 1.3 76.3 - - - +
95I TYR* 1.3 62.2 + - - +
97I TYR* 4.0 0.9 - - - +
98I VAL* 3.1 30.0 + - - +
37J TYR* 3.4 36.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I LEU* 3.8 17.3 - - + +
7I VAL 3.7 3.8 - - - -
8I ASP* 3.5 38.1 - - + -
9I ALA 3.9 1.4 + - - -
32I LEU* 3.5 25.6 - - + -
34I LEU* 3.9 10.7 - - + +
35I THR* 2.7 33.9 + - - +
38I GLU* 2.7 32.5 + - - -
91I TYR 3.7 11.0 - - - -
92I ASP* 3.0 13.7 + - - +
94I SER* 1.3 74.9 - - - +
96I ALA* 1.3 67.1 + - - +
98I VAL* 3.1 1.9 + - - -
99I ALA* 2.9 26.9 + - - +
106I LEU* 4.1 20.0 - - + -
113I LEU* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I VAL* 4.5 3.8 - - + -
86I ARG* 4.4 13.2 - - - +
88I LEU* 4.4 11.7 - - + -
92I ASP 3.3 4.8 + - - +
93I ALA* 4.1 4.9 - - - +
95I TYR* 1.3 78.5 - - - +
97I TYR* 1.3 61.7 + - - +
99I ALA* 4.0 0.2 - - - +
100I GLU* 3.2 32.9 + - - +
106I LEU* 4.0 1.9 - - - +
113I LEU* 4.0 9.4 - - + -
117I THR* 3.3 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I PRO* 3.5 21.8 - - + -
75I PRO* 3.6 25.1 - - + +
78I GLU* 3.3 45.5 + - + +
79I VAL* 4.0 12.1 - - + -
81I ARG* 6.3 1.3 - - - -
82I VAL* 4.1 24.6 - - + +
86I ARG* 6.3 0.2 - - - +
93I ALA 3.0 19.5 + - - +
94I SER 4.0 2.2 - - - +
96I ALA* 1.3 76.5 - - - +
98I VAL* 1.3 59.5 + - + +
100I GLU* 4.2 3.5 - - + +
101I SER* 3.1 55.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I LEU* 3.7 13.0 - - + -
32I LEU* 4.0 13.7 - - + -
71I LEU* 3.6 28.5 - - + -
72I GLU 4.9 4.3 - - - +
74I PRO* 3.1 39.7 - - + -
94I SER 3.1 12.7 + - - +
95I TYR 3.1 1.4 + - - -
97I TYR* 1.3 77.1 - - + +
99I ALA* 1.3 68.3 + - - +
101I SER* 4.3 2.0 - - - -
102I SER* 2.6 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I LEU* 3.8 9.7 - - + +
95I TYR 2.9 20.8 + - - +
96I ALA 4.0 2.9 - - - +
98I VAL* 1.3 77.2 - - - +
100I GLU* 1.3 58.0 + - - +
102I SER* 3.5 0.5 - - - -
103I GLY 2.8 6.1 + - - -
104I LEU* 2.8 51.0 + - - +
106I LEU* 3.7 29.6 - - + +
117I THR* 4.6 4.7 - - + -
118I LYS 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ARG* 2.8 41.2 + - - -
96I ALA 3.2 18.0 + - - +
97I TYR* 4.2 2.7 - - - +
99I ALA* 1.3 78.8 - - - +
101I SER* 1.3 56.6 + - - +
103I GLY* 2.6 27.1 + - - -
104I LEU 4.4 1.8 + - - -
117I THR* 3.9 10.7 - - + -
118I LYS* 2.9 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I TYR* 3.1 53.3 + - - -
98I VAL* 3.9 1.4 + - - -
100I GLU* 1.3 75.7 - - - +
102I SER* 1.3 65.0 + - - +
103I GLY 3.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I LEU* 4.7 2.5 - - - +
98I VAL* 2.6 34.4 + - - +
101I SER* 1.3 81.3 + - - +
103I GLY* 1.3 63.9 + - - +
104I LEU* 3.6 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I ALA 2.8 2.6 + - - -
100I GLU* 2.6 16.5 + - - -
101I SER 3.3 0.6 - - - -
102I SER* 1.3 82.4 - - - +
104I LEU* 1.3 61.1 + - - +
----------------------------------------------------------
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