Contacts of the helix formed by residues 97 - 111 (chain A) in PDB entry 2FL0
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 GLY 97 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 5.0 0.3 - - - +
17A ASN* 4.2 18.6 - - - +
93A LEU* 3.2 12.2 + - - -
94A GLU 4.4 1.1 - - - -
95A GLN 3.0 0.6 - - - -
96A ALA* 1.3 81.2 - - - +
98A LEU* 1.3 65.1 + - - +
99A PRO 3.3 2.5 - - - -
100A ASP* 3.2 15.9 + - - +
101A LEU* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU 3.6 16.5 + - - +
95A GLN* 3.8 6.7 - - + +
97A GLY* 1.3 76.9 - - - +
99A PRO* 1.3 72.2 - - + +
101A LEU* 3.2 11.4 + - + +
102A LYS* 3.1 46.7 + - + +
124A LEU* 3.5 28.3 - - + -
127A GLU* 4.4 16.6 - - + -
128A GLU* 4.3 16.6 - - + +
131A ILE* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLN 2.9 20.4 - - - +
96A ALA* 4.2 4.7 - - - +
97A GLY 3.5 3.6 - - - +
98A LEU* 1.3 92.2 - - + +
100A ASP* 1.3 55.0 + - - +
102A LYS* 2.9 15.3 + - + +
103A ALA* 2.5 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 5.1 1.6 + - - -
13A LYS* 3.3 38.3 + - + +
14A ILE* 3.4 18.6 - - + +
17A ASN* 3.1 21.6 + - - +
96A ALA 4.7 10.6 - - - +
97A GLY 3.2 11.3 + - - +
99A PRO* 1.3 77.7 - - - +
101A LEU* 1.3 52.5 + - - +
103A ALA* 3.0 9.1 + - - +
104A ALA* 2.7 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.7 18.8 - - + +
18A GLU* 5.3 2.0 - - - +
97A GLY 3.3 11.2 + - - +
98A LEU* 3.2 12.0 + - - +
100A ASP* 1.3 78.8 - - - +
102A LYS* 1.3 57.7 + - - +
104A ALA* 3.7 2.6 - - - +
105A ILE* 2.9 37.1 + - - +
120A LEU* 3.8 43.1 - - + +
123A ILE* 3.9 14.8 - - + -
124A LEU* 3.8 24.7 - - + -
127A GLU* 3.7 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.1 44.1 + - + +
99A PRO* 2.9 17.1 + - + +
101A LEU* 1.3 76.0 - - - +
103A ALA* 1.3 64.1 + - - +
105A ILE* 3.4 7.7 + - - +
106A ALA* 3.1 24.9 + - - +
124A LEU* 4.2 17.5 - - + +
128A GLU* 3.9 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 4.3 14.4 + - + -
99A PRO 2.5 21.0 + - - +
100A ASP* 3.5 10.1 - - - +
102A LYS* 1.3 72.7 - - - +
104A ALA* 1.3 57.9 + - - +
106A ALA* 3.6 6.6 + - - +
107A TYR* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 4.1 30.9 + - + +
14A ILE* 4.4 9.9 - - + -
100A ASP 2.7 21.7 + - - +
101A LEU* 3.7 4.3 - - - +
103A ALA* 1.3 72.2 - - - +
105A ILE* 1.3 59.8 + - - +
106A ALA 3.2 0.2 - - - -
107A TYR* 3.1 3.3 + - - +
108A CYS* 2.9 33.1 + - - -
120A LEU* 3.4 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU 2.9 26.3 + - - +
102A LYS* 3.9 5.8 - - - +
104A ALA* 1.3 76.1 - - - +
106A ALA* 1.3 63.0 + - - +
108A CYS* 3.9 4.3 - - - +
109A GLU* 3.1 22.5 + - - +
117A ARG* 3.4 43.9 - - + +
120A LEU* 3.6 24.0 - - + -
121A GLU* 3.9 25.6 - - - +
124A LEU* 3.4 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS 3.1 17.0 + - - +
103A ALA* 3.8 8.1 - - - +
105A ILE* 1.3 77.7 - - - +
107A TYR* 1.3 63.4 + - - +
109A GLU* 3.4 6.7 + - - +
110A SER* 3.1 23.1 + - - -
117A ARG* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP* 5.1 3.3 + - + -
6A ILE* 2.9 54.6 - - + +
7A VAL* 3.6 23.6 - - + -
10A HIS* 3.7 26.0 - + + +
103A ALA 3.2 12.2 + - - +
104A ALA 3.1 8.5 + - - +
106A ALA* 1.3 78.0 - - - +
108A CYS* 1.3 66.0 + - - +
110A SER* 2.8 24.6 + - - -
111A VAL* 3.1 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.1 19.3 - - - -
10A HIS* 6.1 1.6 - - - -
11A LEU* 5.0 2.5 - - - -
104A ALA* 2.9 20.4 + - - +
105A ILE 3.9 4.9 - - - +
107A TYR* 1.3 77.5 - - - +
109A GLU* 1.3 56.3 + - - +
111A VAL* 3.4 7.3 + - - -
112A GLY 3.0 9.5 + - - -
113A ASP* 2.7 46.2 + - + +
116A SER* 3.9 20.6 - - - -
117A ARG* 4.0 9.9 - - + -
120A LEU* 3.8 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE 3.1 18.0 + - - +
106A ALA* 3.6 7.2 - - - +
107A TYR 3.1 0.4 - - - -
108A CYS* 1.3 78.3 - - - +
110A SER* 1.3 62.6 + - - +
111A VAL 3.3 0.9 + - - -
112A GLY* 3.3 10.2 + - - -
114A TYR* 3.7 32.2 + - - -
117A ARG* 2.8 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA 3.1 13.1 + - - -
107A TYR* 2.8 28.5 + - - -
109A GLU* 1.3 77.4 - - - +
111A VAL* 1.3 64.8 + - - +
112A GLY 3.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP* 4.0 27.4 - - - +
7A VAL* 3.6 30.3 - - + -
107A TYR* 3.1 44.4 + - + +
108A CYS 3.7 5.2 - - - +
110A SER* 1.3 83.9 - - - +
112A GLY* 1.3 59.1 + - - +
113A ASP* 4.0 4.7 - - + +
----------------------------------------------------------
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