Contacts of the strand formed by residues 126 - 131 (chain E) in PDB entry 5FLM
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 ILE 126 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E THR* 3.6 4.3 + - - +
101E ARG* 3.3 54.2 - - + +
102E ALA 3.5 21.7 + - - +
118E LEU 5.6 1.1 - - - -
121E MET 4.6 1.3 - - - -
122E ALA* 3.2 30.5 - - + +
123E PRO 5.6 0.2 - - - +
125E TYR* 1.3 71.9 - - - +
127E LEU* 1.3 63.5 + - - +
128E GLU* 5.1 11.3 - - + +
186E LYS* 5.1 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E PHE* 5.4 2.9 - - + -
87E ILE* 3.8 18.8 - - + +
90E TYR* 5.6 2.5 - - + -
91E CYS* 5.1 14.1 - - + +
94E MET* 4.9 11.9 - - + -
102E ALA* 3.6 29.6 - - + +
103E LEU 5.0 0.2 - - - +
104E ILE* 4.5 16.4 - - + -
117E SER 5.9 0.4 - - - +
118E LEU* 3.6 53.6 + - + +
121E MET* 6.0 4.9 - - + -
125E TYR* 4.1 11.6 + - + +
126E ILE* 1.3 85.0 - - - +
128E GLU* 1.3 64.4 + - - +
129E GLN 4.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ARG* 3.1 28.6 + - - -
101E ARG* 4.5 12.9 + - - -
102E ALA 3.8 7.6 + - - +
103E LEU* 3.3 23.5 - - + +
104E ILE* 3.3 24.3 + - - +
118E LEU* 5.1 0.9 - - - -
126E ILE* 5.1 8.7 - - + +
127E LEU* 1.3 79.6 - - - +
129E GLN* 1.3 63.9 + - - +
130E PHE* 3.4 13.6 + - + -
181E ARG* 4.4 2.8 - - - +
184E GLY* 3.8 21.1 - - - +
186E LYS* 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E ILE* 4.1 7.0 - - - -
106E VAL* 4.0 14.2 - - + +
109E GLY* 4.8 0.6 - - - -
110E MET* 3.3 32.6 - - + +
115E LYS* 3.4 33.8 - - - +
118E LEU* 4.3 18.6 - - + +
127E LEU 4.2 1.0 + - - -
128E GLU* 1.3 70.0 - - - +
130E PHE* 1.3 76.1 + - - +
131E LEU* 3.8 25.4 + - + +
134E GLU* 4.6 2.8 - - - +
181E ARG* 4.7 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.8 17.0 - - + -
24E ARG* 3.8 22.4 - - - -
103E LEU* 3.5 33.9 - - + -
104E ILE 2.9 17.3 + - - +
105E VAL* 3.3 3.0 - - + -
106E VAL* 2.6 34.4 + - - +
128E GLU* 3.9 15.3 - - + -
129E GLN* 1.3 89.8 - - - +
131E LEU* 1.3 56.7 + - - +
134E GLU* 4.1 10.8 - - + +
135E LEU* 3.7 39.0 - - + -
181E ARG* 3.8 28.9 - - + -
182E TYR* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E VAL* 4.7 0.4 - - - -
106E VAL* 3.6 6.7 - - + +
107E GLN 5.6 0.4 - - - +
108E GLN* 3.3 29.6 - - - +
109E GLY* 4.7 0.9 - - - -
129E GLN* 3.8 25.0 + - + +
130E PHE* 1.3 80.3 - - - +
132E GLN* 1.3 67.0 + - - +
133E GLN* 3.3 8.1 - - + +
134E GLU* 3.4 47.5 + - + +
135E LEU* 3.7 7.1 + - - +
181E ARG* 5.8 0.7 - - - +
----------------------------------------------------------
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