Contacts of the helix formed by residues 93 - 104 (chain A) in PDB entry 5E1M
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 THR 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 5.0 2.6 + - - +
20A TRP* 3.4 25.3 - - - +
21A LYS* 4.5 11.1 + - + -
91A ASP* 2.9 15.2 + - - +
92A ILE* 1.3 83.5 - - - +
94A GLU* 1.3 63.8 + - - +
95A ASP* 4.0 12.3 - - + +
96A PHE* 3.1 41.7 + - + +
97A LEU* 3.5 10.4 + - - +
116A CYS* 4.3 1.8 - - - -
301A SAH 2.8 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE 3.6 5.1 + - - -
93A THR* 1.3 72.5 - - - +
95A ASP* 1.3 70.8 + - - +
97A LEU* 3.1 8.8 + - + +
98A VAL* 3.0 33.1 + - + +
116A CYS* 3.8 22.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 3.0 40.3 + - + +
25A PRO* 4.5 6.4 - - + +
93A THR* 3.2 10.1 + - + +
94A GLU* 1.3 86.8 - - - +
96A PHE* 1.3 63.1 + - + +
98A VAL* 3.6 9.0 + - - +
99A GLN* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 3.4 40.8 - + - -
23A ILE* 3.4 22.9 - - + -
25A PRO* 3.8 21.5 - - + -
30A MET* 3.7 27.6 - - + -
71A GLY* 3.6 19.3 - - - -
72A ILE* 3.6 10.2 - - + +
91A ASP* 3.8 2.2 - - - +
93A THR* 3.1 27.8 + - + +
95A ASP* 1.3 79.5 - - + +
97A LEU* 1.3 60.8 + - - +
99A GLN* 3.3 1.6 + - - -
100A ALA* 2.8 27.7 + - - +
301A SAH 3.3 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 5.2 0.2 - - + -
71A GLY 3.8 15.7 - - - +
89A MET* 4.1 27.1 - - + -
90A VAL 4.9 0.2 - - - -
91A ASP* 3.9 22.0 - - + +
93A THR 3.5 6.7 + - - +
94A GLU* 3.1 7.9 + - + +
96A PHE* 1.3 73.0 - - - +
98A VAL* 1.3 65.6 + - + +
100A ALA* 3.4 15.9 - - - +
101A LYS* 3.6 12.0 + - - +
114A TYR* 4.1 21.2 - - + +
115A PHE 3.4 36.3 - - - +
116A CYS* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 3.0 31.3 + - + +
95A ASP* 3.8 11.4 - - - +
97A LEU* 1.3 73.7 - - + +
99A GLN* 1.3 61.3 + - - +
101A LYS* 3.2 15.9 + - + +
308A UNX 2.6 30.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 3.5 44.0 + - + +
72A ILE* 4.0 7.4 - - + -
95A ASP 3.0 19.0 + - - +
96A PHE 3.7 4.7 - - - +
98A VAL* 1.3 76.9 - - - +
100A ALA* 1.3 57.6 + - - +
102A THR* 2.8 41.4 + - - +
103A TYR* 2.9 19.1 + - + +
308A UNX 4.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE 3.2 30.4 + - - +
89A MET* 3.9 18.2 - - + -
96A PHE 2.8 12.6 + - - +
97A LEU* 3.4 13.2 - - - +
98A VAL 3.2 0.2 - - - -
99A GLN* 1.3 75.2 - - - +
101A LYS* 1.3 62.1 + - - +
103A TYR* 4.1 1.8 - - - -
104A LEU* 2.9 33.0 + - + +
114A TYR* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 3.7 14.1 - - - +
98A VAL* 3.2 11.4 + - + +
99A GLN 3.1 1.2 + - - -
100A ALA* 1.3 77.9 - - - +
102A THR* 1.3 62.1 + - - +
104A LEU* 4.6 1.1 - - - +
105A GLY* 3.8 14.6 + - - +
108A GLY* 5.9 0.5 - - - -
114A TYR* 3.8 30.5 - - + +
308A UNX 4.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLN* 2.8 25.2 + - - +
101A LYS* 1.3 77.3 - - - +
103A TYR* 1.3 66.4 + - - +
105A GLY* 3.1 14.7 + - - -
308A UNX 2.6 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.6 21.2 - - + +
72A ILE* 3.3 41.1 - - + +
73A GLY 3.5 24.2 - - - -
74A ARG* 3.7 12.3 + - - +
77A LYS* 2.9 46.1 + - + +
78A ARG* 4.1 5.4 + - - +
99A GLN* 2.9 24.6 + - + +
100A ALA* 4.0 0.7 - - - +
102A THR* 1.3 75.5 - - - +
104A LEU* 1.3 63.8 + - + +
105A GLY* 3.4 0.7 + - - -
316A UNX 3.0 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE 4.3 2.7 - - - +
73A GLY 3.6 14.6 - - - +
76A THR* 4.1 5.2 - - + -
77A LYS* 3.6 38.6 - - + +
81A LEU* 4.3 2.9 - - + +
89A MET* 4.0 15.3 - - - -
100A ALA* 2.9 24.4 + - + +
101A LYS 4.8 0.9 - - - +
103A TYR* 1.3 81.0 - - + +
105A GLY* 1.3 65.1 + - - +
106A GLU 3.6 0.7 + - - -
107A GLU* 4.1 0.2 - - - +
108A GLY* 3.3 20.2 + - - +
111A VAL* 3.7 30.3 - - + -
114A TYR* 3.9 11.2 - - - +
309A UNX 3.2 19.9 - - - -
----------------------------------------------------------
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