Contacts of the strand formed by residues 129 - 134 (chain E) in PDB entry 4MNE
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 PHE 129 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E LEU* 3.7 21.1 - - + -
116E GLN* 4.7 1.3 - - - -
118E LEU* 3.3 48.3 + - + +
119E HIS* 3.4 46.8 - + - -
121E CYS* 5.7 1.6 + - + +
127E VAL 3.7 3.5 + - - +
128E GLY* 1.3 71.5 - - - -
130E TYR* 1.3 66.6 + - - +
131E GLY* 3.3 36.8 - - - -
132E ALA* 3.6 11.4 - - + -
141E ILE* 4.0 18.2 - - + -
142E CYS 3.2 12.8 - - - -
143E MET* 4.7 2.7 - - + -
903E 573 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU* 4.8 6.1 - - + -
92E LEU* 4.4 27.5 - - + +
93E VAL 4.5 4.5 + - - -
94E MET* 3.4 42.8 - - + -
119E HIS* 2.7 25.4 + - - -
128E GLY* 5.5 1.3 - - - -
129E PHE* 1.3 79.3 - - - +
131E GLY* 1.3 58.4 + - - +
142E CYS* 2.9 14.0 + - + +
143E MET* 3.3 38.8 - - - -
144E GLU* 3.7 16.4 - - + +
145E HIS 4.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E GLU 6.2 0.9 - - - -
63E LEU* 4.3 15.0 - - - +
119E HIS* 4.2 4.5 - - - -
129E PHE* 3.3 17.7 - - - -
130E TYR* 1.3 83.0 - - - +
132E ALA* 1.3 57.2 + - - -
142E CYS* 2.7 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU* 5.6 2.4 + - - +
112E ILE* 3.8 20.8 - - + +
115E LEU* 3.8 32.3 - - + -
116E GLN* 4.6 10.7 + - - +
129E PHE* 3.6 12.8 - - + -
131E GLY* 1.3 75.6 - - - +
133E PHE* 1.3 66.9 + - - +
140E SER 3.1 12.1 - - - +
141E ILE* 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU* 3.6 35.9 - - + +
64E LYS* 4.0 9.2 - - - -
65E ASP* 3.5 15.0 - - + -
68E PHE* 3.4 36.1 - + - -
96E ARG* 3.3 31.0 - - - -
112E ILE* 3.7 15.7 - - - +
132E ALA* 1.3 78.4 - - - +
134E TYR* 1.3 80.4 + - - +
135E SER* 4.9 3.1 - - - -
139E ILE* 3.5 5.4 - - - -
140E SER* 3.0 46.6 + - - -
142E CYS* 3.8 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LEU 4.2 8.7 + - - -
102E GLU* 5.6 0.3 - - - -
103E ILE* 4.8 11.6 + - + -
108E ARG* 3.4 68.9 + - + -
112E ILE* 5.1 3.1 - - + -
133E PHE* 1.3 86.0 - - - +
135E SER* 1.3 82.7 + - - +
137E GLY* 3.6 18.3 + - - -
138E GLU 3.5 21.3 - - - -
139E ILE* 3.6 19.7 - - + -
----------------------------------------------------------
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