Contacts of the helix formed by residues 100 - 116 (chain A) in PDB entry 2L5E
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 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG* 4.7 0.3 + - - -
95A TYR* 3.4 40.0 - - + -
96A TRP 5.2 0.4 - - - +
97A SER 3.2 3.6 + - - +
98A ALA 3.1 0.6 - - - -
99A SER* 1.3 80.6 - - - +
101A CYS* 1.3 61.7 + - - +
102A MET 3.2 0.7 - - - -
103A GLN* 3.4 22.7 + - - +
104A ASP* 3.1 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.9 10.3 - - + -
86A ILE* 3.5 23.3 - - - -
90A LEU* 3.6 21.5 - - + -
95A TYR* 3.5 21.9 - - + -
97A SER 4.2 0.8 + - - -
98A ALA* 3.0 16.4 + - - +
100A GLU* 1.3 74.9 - - - +
102A MET* 1.3 57.5 + - - +
103A GLN 2.9 6.2 + - - -
104A ASP* 2.9 27.1 - - - +
105A PHE* 2.9 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.8 30.5 - - + +
98A ALA 3.2 8.3 + - - +
99A SER* 3.4 19.1 - - - +
101A CYS* 1.3 76.9 - - - +
103A GLN* 1.3 56.4 + - - +
105A PHE* 4.3 5.6 - - - +
106A ASN* 3.2 27.8 + - - +
133A PHE* 4.6 11.5 - - + -
137A VAL* 3.6 33.2 - - + -
140A MET* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG* 5.7 1.6 - - - +
99A SER 4.4 1.0 + - - +
100A GLU* 3.4 22.8 + - - +
101A CYS 2.9 1.0 - - - -
102A MET* 1.3 75.2 - - - +
104A ASP* 1.3 68.6 + - - +
106A ASN* 3.1 40.6 + - - +
107A THR* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 4.6 18.3 - - - +
86A ILE* 3.6 22.0 - - + +
89A ARG* 2.8 26.7 + - - +
95A TYR* 2.8 23.4 + - - -
100A GLU 3.1 16.8 - - - +
101A CYS* 2.9 25.4 - - - +
103A GLN* 1.3 72.5 - - - +
105A PHE* 1.3 63.4 + - - +
107A THR* 3.3 6.8 + - - +
108A MET* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.9 22.4 - - + -
46A VAL* 4.0 15.0 - - + -
47A VAL* 3.5 44.6 - - + -
50A LEU* 3.5 26.7 - - + -
83A MET* 5.0 0.7 - - + -
86A ILE* 3.5 33.4 - - + +
101A CYS* 2.9 17.0 + - - +
102A MET* 4.3 2.9 - - - +
104A ASP* 1.3 79.6 + - - +
106A ASN* 1.3 61.0 + - - +
108A MET* 3.5 22.2 - - + +
109A PHE* 3.7 17.1 + + - -
133A PHE* 3.5 32.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A MET 3.2 17.5 + - - +
103A GLN* 3.1 31.1 + - - -
105A PHE* 1.3 80.0 - - - +
107A THR* 1.3 66.1 + - - +
109A PHE* 3.5 7.7 + - - +
110A THR* 2.7 39.5 + - - +
133A PHE* 5.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 5.4 0.4 - - + -
78A LYS* 5.8 0.4 - - + -
79A ASN* 3.1 59.9 + - + +
81A MET* 5.0 2.5 - - + -
103A GLN* 3.1 16.1 + - - +
104A ASP* 3.3 10.0 + - - -
106A ASN* 1.3 86.0 + - - +
108A MET* 1.3 57.6 + - - +
110A THR* 3.0 8.2 + - - +
111A ASN* 2.7 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.7 30.1 - - + -
59A PHE* 3.6 41.2 - - + -
81A MET* 3.8 17.4 - - + +
82A ASP 3.1 24.9 - - - +
83A MET* 3.8 16.8 - - + -
86A ILE* 3.9 5.4 - - + -
104A ASP 3.0 15.2 + - - +
105A PHE* 3.5 13.7 - - + +
106A ASN 3.4 0.4 - - - -
107A THR* 1.3 76.6 - - - +
109A PHE* 1.3 83.4 + - + +
111A ASN* 3.3 20.6 + - - +
112A CYS* 3.6 2.3 + - - +
129A LEU* 5.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.0 10.8 - - + -
59A PHE* 5.1 0.4 - + - -
105A PHE* 3.7 19.5 + + - -
106A ASN* 3.5 9.5 + - - +
107A THR 3.1 0.4 - - - -
108A MET* 1.3 105.4 - - + +
110A THR* 1.3 66.3 + - + +
112A CYS* 3.3 7.9 + - - +
113A TYR* 3.2 37.7 + - + -
126A ALA* 3.4 38.1 - - + -
129A LEU* 3.7 15.0 - - + -
130A GLU* 3.6 32.5 - - + +
133A PHE* 3.9 31.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 2.7 27.9 + - - +
107A THR* 3.0 15.8 + - - +
109A PHE* 1.3 74.8 - - + +
111A ASN* 1.3 64.5 + - - +
113A TYR* 2.9 16.8 + - + +
114A ILE* 2.9 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 4.5 7.3 - - - -
63A VAL* 5.9 0.4 - - - +
73A TYR* 2.7 42.8 + - - -
77A ILE* 3.4 32.9 - - + +
79A ASN 4.6 3.8 - - - +
81A MET 3.3 19.6 + - - -
107A THR* 2.7 25.3 + - + +
108A MET* 3.3 15.9 + - - -
110A THR* 1.3 73.0 - - - +
112A CYS* 1.3 62.4 + - - +
114A ILE* 4.3 3.1 - - - +
115A TYR* 3.0 27.9 + - - +
312B ALY 5.1 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 3.7 22.4 - - + -
108A MET 3.6 1.3 + - - +
109A PHE 3.3 8.4 + - - +
110A THR 3.2 0.4 - - - -
111A ASN* 1.3 84.2 - - - +
113A TYR* 1.3 60.2 + - - +
116A ASN* 3.0 46.0 + - - +
122A ILE* 3.5 30.1 - - + -
123A VAL* 3.6 26.8 - - - +
126A ALA* 3.8 10.3 - - + -
312B ALY 4.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.2 30.1 - - + -
110A THR* 2.9 18.0 + - + +
112A CYS* 1.3 78.0 - - - +
114A ILE* 1.3 60.6 + - + +
116A ASN 3.0 14.2 - - - +
117A LYS 5.3 0.5 - - - -
118A PRO* 5.3 2.9 - - - +
123A VAL* 4.0 22.6 - - + +
126A ALA* 3.5 23.5 + - + +
127A GLN* 3.4 39.3 + - + +
130A GLU* 3.2 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 4.6 13.8 - - + +
77A ILE* 3.9 15.7 - - + -
78A LYS* 5.4 13.7 - - + -
110A THR* 2.9 36.4 + - + +
111A ASN* 3.8 6.5 - - - +
113A TYR* 1.3 82.2 - - + +
115A TYR* 1.3 67.6 + - - +
116A ASN 3.5 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.2 5.3 - - + +
72A ASP* 2.7 27.8 + - - -
73A TYR* 3.5 44.3 - + + +
76A ILE* 3.8 34.8 - - + -
77A ILE* 3.8 19.5 - - + -
111A ASN 3.0 16.1 + - - +
114A ILE* 1.3 79.9 - - - +
116A ASN* 1.3 73.3 + - - +
117A LYS 4.2 0.3 + - - -
312B ALY 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 4.7 0.2 + - - -
112A CYS* 3.0 29.5 + - - +
113A TYR 3.0 22.7 - - - +
114A ILE 3.8 2.4 - - - +
115A TYR* 1.3 88.3 - - - +
117A LYS* 1.3 63.7 + - - +
118A PRO* 3.9 0.5 - - - +
120A ASP* 4.2 6.9 - - + +
122A ILE* 3.5 26.4 - - + +
123A VAL* 4.0 5.7 - - + +
312B ALY 2.8 57.0 + - - +
----------------------------------------------------------
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