Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 2FOL
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 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS 3.7 2.4 + - - +
11A LEU* 3.3 10.3 - - - +
12A LEU 3.3 18.9 + - - -
81A ALA* 3.4 1.6 - - - +
82A HIS* 1.3 83.3 - - - +
84A ILE* 1.3 66.1 + - - +
114A VAL* 3.7 0.7 - - - -
115A ASN* 3.0 12.8 - - - -
165A MET* 3.7 22.0 - - - -
169A ILE* 3.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.2 27.4 - - + +
14A ILE* 3.1 45.1 - - + -
78A TYR* 4.0 25.1 - - + +
81A ALA* 4.0 6.3 - - + -
83A GLY* 1.3 78.1 - - - +
85A ILE* 1.3 62.6 + - - +
86A VAL* 4.0 0.9 + - - +
106A ILE* 3.6 19.3 - - + -
110A ALA* 4.1 13.0 - - + -
114A VAL* 3.8 19.7 - - + -
115A ASN 2.7 10.9 + - - +
116A LYS* 3.4 6.4 - - - +
117A LEU 3.3 11.1 + - - +
165A MET* 3.1 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.9 5.8 - - + -
12A LEU 2.7 11.4 + - - +
13A LEU* 3.4 29.4 - - + -
14A ILE* 2.8 33.3 + - - +
24A LEU* 6.3 0.4 - - + -
83A GLY 5.5 0.2 - - - +
84A ILE* 1.3 77.7 - - - +
86A VAL* 1.3 59.4 + - - +
87A VAL* 3.7 8.5 + - + +
117A LEU* 3.5 18.4 - - + +
119A VAL* 3.5 30.1 - - + -
161A SER* 4.8 4.3 - - - +
162A PHE* 3.7 28.3 - - + -
165A MET* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.6 15.3 - - + +
84A ILE* 4.3 2.7 - - + +
85A ILE* 1.3 72.0 - - - +
87A VAL* 1.3 62.4 + - - +
99A VAL* 3.8 31.0 - - + +
102A TRP* 3.8 25.4 - - + +
103A LEU* 4.2 12.3 - - + -
106A ILE* 3.6 31.0 - - + -
116A LYS* 5.7 2.5 - - + -
117A LEU 2.9 14.1 + - - +
118A LEU* 3.3 13.5 - - + +
119A VAL 3.0 21.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.7 7.4 - - + -
14A ILE 2.9 16.6 + - - +
15A GLY* 3.4 20.0 - - - -
16A ASP 4.2 2.1 + - - -
19A VAL* 3.9 13.9 - - + +
21A LYS* 3.8 19.7 - - + -
24A LEU* 3.9 22.0 - - + -
85A ILE* 4.2 19.1 - - + +
86A VAL* 1.3 81.5 - - - +
88A TYR* 1.3 77.5 + - - +
95A SER 5.0 0.9 - - - +
99A VAL* 4.5 1.9 - - - +
102A TRP* 5.1 0.9 - - - -
119A VAL* 3.3 11.7 - - + +
121A ASN* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.1 13.5 - - - -
87A VAL* 1.3 79.1 - - - +
89A ASP* 1.3 74.5 + - - +
90A VAL* 4.3 5.3 - - - +
95A SER* 3.6 22.4 - - - +
96A PHE* 3.5 28.9 - + + -
99A VAL* 3.9 4.0 - - + -
118A LEU* 3.5 32.5 - - + -
119A VAL 2.7 23.5 + - - +
120A GLY* 3.5 23.4 - - - -
121A ASN* 2.7 30.8 + - - +
131A VAL* 3.5 30.4 + - + +
136A ALA* 3.0 25.9 - - + +
147A PHE* 3.6 10.5 - + - -
149A GLU* 5.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.8 2.9 - - - +
19A VAL* 4.2 17.7 - - + -
88A TYR* 1.3 82.2 - - - +
90A VAL* 1.3 60.4 + - - +
91A THR* 2.7 34.9 + - - +
92A ASP* 2.9 40.5 + - + +
95A SER* 3.2 12.7 + - - +
121A ASN 3.7 4.5 - - - -
122A LYS* 3.1 38.8 + - + +
131A VAL* 3.9 0.9 - - - +
----------------------------------------------------------
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