Contacts of the strand formed by residues 100 - 107 (chain E) in PDB entry 5AQP
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 ARG 100 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ARG 4.8 3.4 - - - +
77E ARG* 4.0 15.7 - - - +
78E PHE* 4.0 3.4 - - - -
95E VAL 3.6 0.3 - - - +
96E ASN* 3.7 0.3 - - - -
97E ASP* 2.8 41.8 + - - +
98E ALA 4.5 2.9 - - - +
99E GLY* 1.3 80.8 - - - +
101E PRO* 1.4 70.7 - - + +
115E TYR* 4.1 30.3 - - + -
117E GLU* 6.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LEU* 4.0 29.8 - - + +
76E ARG 3.1 29.8 - - - +
77E ARG 4.5 1.1 - - - +
78E PHE* 3.6 20.4 - - + +
83E VAL* 4.4 4.0 - - + -
94E VAL* 3.9 19.7 - - + -
95E VAL 3.3 7.4 - - - +
100E ARG* 1.4 84.4 - - + +
102E LYS* 1.3 65.3 + - - +
115E TYR* 3.9 4.0 - - - -
116E PRO* 3.4 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LEU* 6.0 0.2 - - - -
94E VAL* 3.4 4.7 - - - -
95E VAL* 2.8 45.7 + - + +
97E ASP* 3.4 35.2 + - + +
101E PRO* 1.3 79.2 - - - +
103E VAL* 1.3 64.6 + - - +
113E SER* 2.8 37.1 + - - +
114E PHE 3.3 23.8 - - - +
115E TYR* 3.7 37.1 + - + +
116E PRO* 4.8 1.6 - - - -
118E GLU* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E PHE* 5.6 0.2 - - + -
67E VAL* 3.9 28.5 - - + -
70E ALA* 6.3 0.7 - - + -
73E LEU* 4.0 19.5 - - + -
92E PHE* 3.7 29.2 - - + -
93E MET 3.3 7.0 - - - +
94E VAL* 4.4 1.3 - - + -
102E LYS* 1.3 71.7 - - - +
104E GLN* 1.3 61.3 + - - +
105E VAL* 4.1 2.1 + - + -
112E LYS 3.9 0.3 - - - +
113E SER* 3.1 4.0 - - - -
114E PHE* 2.8 52.6 + - + +
115E TYR 5.6 0.2 - - - -
116E PRO* 5.6 3.1 - - + +
119E VAL* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E THR 4.8 1.9 - - - +
92E PHE* 5.0 0.2 - - - +
93E MET* 2.8 63.9 + - + +
95E VAL* 3.7 33.2 - - + +
102E LYS 3.7 0.4 + - - -
103E VAL* 1.3 73.4 - - - +
105E VAL* 1.3 65.2 - - - +
111E THR* 3.8 30.1 - - + +
112E LYS 3.5 8.1 - - - +
113E SER* 4.3 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E PHE* 3.3 40.4 - - + -
64E THR 4.3 4.3 - - - +
65E ASN* 3.9 20.0 - - - +
67E VAL* 3.8 29.4 - - + -
92E PHE* 5.0 1.1 - - + -
103E VAL* 5.0 2.2 - - + -
104E GLN* 1.3 81.6 - - - +
106E GLU* 1.4 60.3 + - - +
107E TYR* 4.4 2.5 - - + -
110E GLU 3.7 0.2 - - - +
111E THR* 3.5 6.8 - - - +
112E LYS 2.8 41.2 + - - +
114E PHE* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E PHE* 3.5 24.1 - - - +
45E THR 4.3 2.6 - - - +
65E ASN* 2.9 26.9 + - - +
105E VAL* 1.4 69.3 - - - +
107E TYR* 1.3 58.8 + - - +
108E LYS 4.2 0.7 - - - -
109E GLY* 5.1 5.2 - - - +
110E GLU 3.4 11.7 - - - +
111E THR* 4.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E PHE* 3.6 35.9 - + + -
45E THR 3.8 5.8 - - - -
48E GLU 3.8 16.8 - - - -
49E ARG* 3.6 28.8 + - + +
105E VAL* 3.9 6.2 - - + -
106E GLU* 1.3 73.8 - - - +
108E LYS* 1.4 108.8 + - + +
110E GLU* 2.9 28.3 + - - +
112E LYS* 4.6 9.7 - - + +
114E PHE* 4.5 13.2 - + - -
----------------------------------------------------------
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