Contacts of the strand formed by residues 100 - 104 (chain E) in PDB entry 4LQL
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 LEU 100 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E MET* 5.2 4.7 - - + -
76E VAL* 3.4 31.4 - - + +
78E THR* 4.8 14.4 - - - -
89E TRP* 6.1 5.6 - - + -
93E THR* 4.3 12.8 - - - +
96E LEU* 3.4 36.8 - - + -
98E LYS 3.3 2.3 + - - +
99E PRO* 1.3 72.4 - - - +
101E LEU* 1.3 65.8 + - - +
102E HIS 4.3 1.1 - - - +
137E ASN* 6.0 5.6 - - + -
142E VAL* 4.9 12.6 - - + -
143E PRO 4.5 7.3 + - - +
144E ALA* 3.4 28.6 - - + +
145E ALA 3.5 8.3 + - - -
163E TRP* 4.6 3.6 + - - -
465E LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E VAL 3.1 14.4 + - - +
77E ILE* 3.6 9.8 - - + -
78E THR* 2.7 31.2 + - - -
100E LEU* 1.3 79.0 - - - +
102E HIS* 1.3 65.2 + - - +
103E LEU* 2.7 14.7 + - + +
145E ALA* 3.5 40.8 - - + +
146E SER 3.6 2.5 - - - +
147E VAL* 3.7 13.2 - - + -
160E ILE* 3.5 32.1 - - + -
163E TRP* 4.2 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D MET* 5.9 2.9 - - + -
78E THR* 3.3 10.1 - - - -
79E TRP* 5.8 0.7 - - - -
80E MET 6.2 0.2 - - - -
100E LEU* 4.3 2.6 - - - +
101E LEU* 1.3 73.3 - - - +
103E LEU* 1.3 60.0 + - - +
104E ALA* 3.2 13.1 + - + +
130E ASP* 4.1 33.9 - - + -
133E TYR* 4.9 15.5 - + + -
134E ALA* 5.0 9.0 - - + -
144E ALA* 5.7 1.6 - - - +
145E ALA 4.0 4.9 + - - +
146E SER* 3.8 15.3 + - - +
147E VAL 3.5 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E PHE* 5.1 10.3 - - + -
77E ILE* 4.7 7.6 - - + -
78E THR 2.4 22.1 + - - +
79E TRP* 3.0 22.9 - - + +
101E LEU* 2.7 18.8 + - + +
102E HIS* 1.3 69.9 - - - +
104E ALA* 1.3 55.7 + - - +
105E THR* 3.0 25.2 + - + -
147E VAL* 3.9 9.6 - - + -
151E TRP* 6.1 2.5 - - + -
160E ILE* 4.4 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D MET* 5.4 10.1 - - + -
79E TRP* 4.2 4.0 - - - -
102E HIS* 3.2 11.3 + - + +
103E LEU* 1.3 69.6 - - - +
105E THR* 1.3 59.7 + - - +
130E ASP* 4.5 20.6 - - + +
146E SER* 6.5 0.4 - - - -
147E VAL 3.0 18.7 + - - +
148E TYR* 3.6 9.8 - - + -
149E GLY 3.3 23.9 + - - +
----------------------------------------------------------
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