Contacts of the strand formed by residues 140 - 146 (chain E) in PDB entry 3QS7
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 GLU 140 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E VAL 4.1 1.1 - - - +
107E PHE 3.4 2.8 - - - +
108E LYS* 3.1 35.0 + - - +
139E GLY* 1.3 67.7 - - - -
141E TYR* 1.4 59.8 + - - +
142E LEU 4.2 0.7 - - - -
156E PHE 3.7 4.9 - - - -
157E THR* 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E VAL 3.7 2.5 - - - +
107E PHE* 3.4 22.9 - - + -
108E LYS* 3.4 24.3 - - + +
136E THR 3.8 3.5 + - - -
137E GLN* 3.3 10.9 - - + -
138E ALA* 2.9 34.0 + - - -
139E GLY 3.4 34.1 - - - -
140E GLU* 1.4 74.0 - - - +
142E LEU* 1.3 60.4 + - - +
155E LEU* 4.5 0.9 - - - -
156E PHE* 2.9 53.8 + - + +
158E VAL* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TRP* 3.7 4.3 - - - +
106E VAL* 2.9 47.1 + - + +
140E GLU 4.2 0.6 - - - -
141E TYR* 1.3 74.7 - - - +
143E LEU* 1.3 63.3 + - - +
144E PHE 5.4 0.2 - - - +
153E THR* 6.5 0.4 - - - -
154E ILE 3.1 14.8 - - - +
155E LEU* 4.1 8.1 - - + +
156E PHE* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E VAL* 4.3 9.6 - - + -
103E CYS* 3.9 24.0 - - + -
104E LEU 3.6 19.3 - - - +
105E TRP* 4.0 12.1 - - + +
114E CYS* 4.6 2.7 - - + -
126E VAL* 3.8 28.0 - - + -
127E SER* 5.3 2.2 - - - +
142E LEU* 1.3 74.9 - - - +
144E PHE* 1.4 59.8 + - - +
145E ILE* 3.9 9.1 + - + +
153E THR* 3.7 1.4 - - - -
154E ILE* 2.9 63.6 + - + +
156E PHE* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E CYS* 3.3 4.0 - - - +
104E LEU* 2.9 43.3 + - + +
106E VAL* 5.8 2.6 - - + +
142E LEU* 4.3 1.2 - - - +
143E LEU* 1.4 70.8 - - - +
145E ILE* 1.3 60.4 + - - +
152E TYR 3.5 10.8 - - - +
153E THR* 4.1 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ILE* 3.9 20.0 - - + -
102E SER 3.4 8.3 - - - +
103E CYS* 3.6 29.4 - - + -
126E VAL* 4.9 5.6 - - + -
143E LEU* 3.9 28.5 + - + +
144E PHE* 1.3 72.4 - - - +
146E GLN* 1.4 64.5 + - - +
147E SER 5.0 0.9 - - - +
150E THR* 6.0 2.5 - - - -
151E ASN* 3.4 4.4 - - - +
152E TYR* 2.9 49.5 + - + +
154E ILE* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ILE* 3.2 4.9 - - - +
102E SER* 2.9 39.2 + - - +
145E ILE* 1.4 77.5 - - - +
147E SER* 1.4 61.7 + - - +
150E THR 3.3 10.3 - - - +
151E ASN* 4.8 3.8 - - + -
----------------------------------------------------------
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