Contacts of the helix formed by residues 92 - 102 (chain I) in PDB entry 2FRV
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 MET 92 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I HIS 4.7 0.4 - - - +
14I ASN* 2.9 55.4 - - - +
15I ALA 3.8 3.1 - - - -
76I ILE* 4.3 1.6 - - + -
77I PRO* 4.1 16.6 - - + -
82I GLY 4.6 0.8 + - - -
85I GLY* 3.0 43.1 + - - +
86I LYS 3.7 6.1 - - - +
87I VAL* 4.4 12.1 - - + -
90I ARG 3.4 0.4 + - - -
91I ASN* 1.3 68.2 - - - +
93I TYR* 1.3 65.8 + - - +
94I ASP 3.3 0.2 + - - -
95I ILE* 3.3 10.2 + - + +
96I CYS* 3.1 27.5 + - - -
20J HIS* 3.6 32.1 - - + +
41J LEU* 4.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I ILE* 3.5 23.5 - - + +
77I PRO 4.2 12.0 + - - +
78I MET* 3.7 26.9 - - + -
81I GLY 5.8 1.8 - - - +
82I GLY* 5.4 2.0 + - - -
91I ASN* 3.2 6.8 - - + +
92I MET* 1.3 79.1 - - - +
94I ASP* 1.3 70.1 + - - +
96I CYS* 3.8 1.8 - - - +
97I ALA* 2.9 39.1 + - + +
134I ALA 3.7 10.1 - - - -
135I LEU* 3.3 26.7 - - + -
137I LYS* 2.8 34.5 + - - -
138I LEU* 3.9 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I ARG* 3.8 19.7 + - + +
91I ASN* 2.8 36.1 + - - +
93I TYR* 1.3 88.5 - - - +
95I ILE* 1.3 65.1 + - - +
97I ALA* 3.3 5.4 + - - +
98I GLU* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LEU* 4.3 17.9 - - + -
57I GLU* 5.7 4.7 - - - +
60I LEU* 4.3 11.9 - - + -
87I VAL* 3.6 37.0 - - + +
90I ARG* 3.4 55.8 - - + +
91I ASN 3.1 10.1 + - - +
92I MET* 3.3 8.7 + - + +
94I ASP* 1.3 76.8 - - - +
96I CYS* 1.3 56.4 + - - +
98I GLU* 3.2 2.1 + - - +
99I VAL* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LEU* 4.0 21.3 - - - -
14I ASN* 3.4 31.4 - - - -
72I ILE* 4.4 7.2 - - + -
76I ILE* 3.9 17.0 - - + -
92I MET 3.1 19.8 + - - +
93I TYR 3.8 3.4 - - - +
95I ILE* 1.3 72.5 - - - +
97I ALA* 1.3 64.2 + - - +
99I VAL 4.4 0.4 - - - +
100I ALA* 2.9 36.9 + - - +
135I LEU* 3.7 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I TYR* 2.9 36.0 + - + +
94I ASP* 3.3 6.0 + - - +
96I CYS* 1.3 77.2 - - - +
98I GLU* 1.3 56.9 + - - +
101I PRO* 2.9 24.9 - - - +
135I LEU* 4.4 2.2 - - + +
138I LEU* 3.4 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I LEU* 6.5 0.4 - - - -
61I HIS* 4.8 10.4 + - - -
64I ILE* 3.7 25.9 - - + +
90I ARG* 2.7 38.6 + - - +
94I ASP 3.1 10.9 + - - +
95I ILE* 3.5 8.3 - - - +
96I CYS 3.1 0.2 - - - -
97I ALA* 1.3 79.8 - - - +
99I VAL* 1.3 64.4 + - + +
101I PRO* 3.8 2.4 - - - +
102I LYS* 3.1 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I VAL* 4.2 6.5 - - + -
12I LEU* 4.1 12.6 - - + -
60I LEU* 4.4 11.0 - - + -
64I ILE* 3.9 31.0 - - + -
68I PHE* 3.7 17.1 - - + -
70I CYS* 4.0 20.6 - - - -
95I ILE* 2.9 36.8 + - + +
98I GLU* 1.3 76.7 - - + +
100I ALA* 1.3 66.2 + - - +
102I LYS* 3.0 22.6 + - - +
103I ALA 3.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I CYS* 4.3 8.3 - - - -
72I ILE* 4.1 17.7 - - + -
96I CYS* 2.9 20.2 + - - +
99I VAL* 1.3 76.7 - - - +
101I PRO* 1.3 67.7 - - + +
103I ALA* 3.2 21.1 + - - +
106I VAL* 3.6 13.9 - - + +
135I LEU* 4.0 12.3 - - + -
140I VAL* 3.9 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 101 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I CYS 3.4 0.9 - - - +
97I ALA 2.9 29.2 - - - +
98I GLU 3.8 2.7 - - - +
99I VAL 3.4 3.6 - - - -
100I ALA* 1.3 95.5 - - + +
102I LYS* 1.3 60.7 + - + +
103I ALA 3.5 4.9 + - - +
138I LEU* 4.0 37.2 - - + +
139I GLY 6.3 0.2 - - - -
140I VAL* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I ILE* 3.9 42.2 - - + +
66I GLY 4.4 5.5 - - - +
68I PHE* 3.6 16.9 - - + -
98I GLU* 3.1 33.5 + - - +
99I VAL 3.0 7.1 + - - +
101I PRO* 1.3 78.3 - - + +
103I ALA* 1.3 61.3 + - - +
104I LYS* 4.5 7.4 - - - -
----------------------------------------------------------
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