Contacts of the strand formed by residues 106 - 115 (chain H) in PDB entry 1E50
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 VAL 106 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLN* 3.6 18.4 - - + +
11H LYS* 3.9 19.1 - - + -
12H PHE* 4.0 16.8 - - + +
18H PHE* 3.3 34.5 - - + -
102H ILE* 3.8 3.3 - - - +
103H LEU 2.9 24.0 + - - +
104H ASN 3.5 5.6 - - - +
105H GLY* 1.3 81.9 - - - +
107H CYS* 1.3 64.6 + - - +
108H VAL* 3.2 27.2 + - + +
127H PHE* 4.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 4.1 1.8 - - - -
8H GLN* 2.7 23.4 + - - +
101H MET 3.7 5.8 - - - -
102H ILE* 4.0 8.1 - - - +
106H VAL* 1.3 70.1 - - - +
108H VAL* 1.3 63.7 + - - +
127H PHE* 3.5 9.7 - - - -
128H ASP 3.0 20.1 + - - +
131H ARG* 3.1 31.9 - - - +
132H ALA* 3.6 20.0 - - + +
135H GLU* 3.3 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H PHE* 3.8 21.5 - - + -
18H PHE* 4.2 7.2 - - + -
100H PRO* 3.7 0.7 - - - +
101H MET* 3.0 42.6 + - + +
103H LEU* 4.0 13.0 - - + -
106H VAL* 3.2 32.7 + - + +
107H CYS* 1.3 73.5 - - - +
109H ILE* 1.3 66.6 + - - +
125H LEU* 4.1 22.4 - - + -
126H GLU 3.1 11.2 - - - +
128H ASP 4.0 0.9 - - - +
131H ARG* 2.8 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H LYS* 3.7 44.0 - - + +
99H ALA 3.6 8.1 - - - +
100H PRO* 4.9 6.5 - - + -
108H VAL* 1.3 78.3 - - - +
110H TRP* 1.3 63.3 + - - +
111H LYS* 3.8 20.9 + - + +
125H LEU* 3.5 1.3 - - - -
126H GLU* 2.7 47.2 + - + +
127H PHE 5.5 1.3 - - - +
128H ASP* 3.1 41.1 - - + +
131H ARG* 4.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H ILE* 3.8 31.8 - - + +
55H ILE* 3.6 35.7 + - + -
57H PHE* 3.4 26.2 - + - -
64H LEU* 3.6 15.6 - - + +
66H LEU* 3.5 30.3 - - + +
97H LEU* 3.7 25.8 - - + -
98H LYS* 3.3 3.3 - - - -
99H ALA* 2.8 50.0 + - + +
101H MET* 4.9 3.8 - - - -
108H VAL* 5.0 0.4 - - - +
109H ILE* 1.3 72.9 - - - +
111H LYS* 1.3 66.0 + - - +
112H GLY* 3.6 19.5 - - - -
114H ILE* 5.5 0.4 - - + -
123H GLY* 5.0 0.4 - - - -
124H CYS 3.5 5.4 - - - -
125H LEU* 3.4 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H LEU 3.3 5.6 - - - +
98H LYS* 4.1 25.1 - - + +
109H ILE* 3.8 25.8 - - + +
110H TRP* 1.3 82.8 - - - +
112H GLY* 1.3 58.8 + - - +
123H GLY* 3.1 1.4 - - - -
124H CYS* 2.8 38.1 + - - +
126H GLU* 2.9 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H TYR* 3.4 6.2 - - - +
97H LEU* 2.6 40.7 + - - +
110H TRP* 3.6 13.7 - - - -
111H LYS* 1.3 75.6 - - - +
113H TRP* 1.3 60.4 + - - -
122H MET 3.1 13.7 - - - -
123H GLY* 3.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 113 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLU* 4.3 8.8 + - - -
27H ILE* 3.4 2.5 - - - +
94H LYS* 3.5 37.4 - - + +
95H VAL 3.0 13.5 - - - +
96H TYR* 3.5 44.9 + + + -
97H LEU* 5.5 1.1 - - - -
112H GLY* 1.3 76.3 - - - +
114H ILE* 1.3 75.0 + - - +
115H ASP* 4.2 10.1 - - + -
120H ASP 4.1 4.0 - - - -
121H GLY* 3.3 21.0 - - - -
122H MET* 2.8 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H ILE* 4.1 10.8 - - + -
28H LYS* 4.6 0.9 - - - -
29H TYR* 4.0 15.7 - - + +
44H PHE* 3.4 36.8 - - + -
55H ILE* 3.3 42.0 - - + -
94H LYS* 2.9 21.1 - - - +
95H VAL* 2.9 20.4 + - + +
97H LEU* 4.9 2.4 - - + +
113H TRP* 1.3 82.1 - - - +
115H ASP* 1.3 75.6 + - - +
116H LEU 3.3 0.5 + - - -
119H LEU* 3.8 12.1 - - - +
120H ASP 3.3 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H GLY 4.3 4.9 - - - +
94H LYS* 3.9 10.8 - - - +
113H TRP* 4.1 11.4 - - + -
114H ILE* 1.3 71.0 - - - +
116H LEU* 1.3 60.1 + - - +
117H GLN* 2.8 36.3 + - - +
118H ARG* 2.8 36.4 + - + +
119H LEU* 2.6 32.4 + - - -
120H ASP 2.7 16.7 + - - +
----------------------------------------------------------
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