Contacts of the strand formed by residues 105 - 116 (chain A) in PDB entry 2L0W
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 CYS 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY* 6.2 2.0 - - - -
72A PRO* 6.0 5.8 - - - -
73A ARG* 5.9 10.8 - - + -
97A ALA* 5.9 4.5 - - + -
98A PHE 3.4 8.7 - - - +
99A TYR* 4.0 19.7 - - - -
103A GLY 4.6 5.4 - - - -
104A SER* 1.3 82.0 - - - +
106A PHE* 1.3 68.9 + - - +
134A GLU* 4.1 5.0 - - - +
135A LYS* 3.1 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.7 33.4 - - + -
52A CYS* 5.3 2.9 - - + -
69A LEU* 6.5 0.2 - - + -
97A ALA* 3.4 3.3 - - - -
98A PHE* 3.0 52.0 + + + +
99A TYR 4.6 2.7 - - - -
100A ARG* 3.7 41.7 - - + -
104A SER* 5.4 0.7 - - - -
105A CYS* 1.3 81.1 - - - +
107A LEU* 1.3 71.9 + - - +
108A CYS* 3.8 23.8 - - + -
131A VAL* 3.8 28.7 - - + -
133A MET 3.6 11.4 - - - +
134A GLU* 3.9 13.0 - - + -
135A LYS* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 4.1 15.3 - - - +
95A GLU* 4.4 14.4 - - + +
96A ILE* 3.5 29.8 - - - +
97A ALA* 3.6 11.7 - - + +
106A PHE* 1.3 70.9 - - - +
108A CYS* 1.3 55.4 + - - +
131A VAL* 3.6 5.7 - - - +
132A VAL* 2.8 48.3 + - + -
133A MET* 2.8 27.0 + - + +
135A LYS* 3.8 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 5.3 1.3 - - - -
95A GLU* 3.5 3.2 - - - +
96A ILE* 2.8 38.6 + - + +
98A PHE* 3.5 38.8 - - + -
106A PHE* 3.5 17.6 + - + -
107A LEU* 1.3 73.1 - - - +
109A LEU* 1.3 75.4 + - - +
110A VAL* 4.3 0.2 - - - -
129A PHE* 3.8 24.7 - - - -
130A GLU 3.3 11.0 - - - -
132A VAL* 4.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 4.2 44.6 - - + +
94A VAL 3.6 19.5 - - - +
95A GLU* 4.1 16.8 - - + +
107A LEU 4.2 0.2 + - - -
108A CYS* 1.3 71.4 - - - +
110A VAL* 1.3 61.6 + - - +
111A ASP* 4.1 3.2 + - + +
128A ASN 3.6 1.6 - - - +
129A PHE* 3.5 5.9 - - - -
130A GLU* 2.8 55.7 + - + +
132A VAL* 4.6 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 3.7 35.7 - - + -
92A ARG 3.9 1.2 - - - +
93A LYS* 3.3 2.8 - - - +
94A VAL* 2.8 41.9 + - - +
96A ILE* 3.9 7.4 - - + -
98A PHE* 3.8 28.3 - - + -
108A CYS* 4.3 0.4 - - - -
109A LEU* 1.3 75.1 - - - +
111A ASP* 1.3 61.2 + - - +
112A VAL* 5.0 1.1 - - + +
127A LEU* 4.0 25.1 - - + -
128A ASN 3.4 5.2 - - - +
129A PHE* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 3.5 27.2 - - - +
92A ARG 3.4 4.0 - - - +
93A LYS* 3.5 30.1 - - + +
109A LEU* 4.1 3.8 - - + +
110A VAL* 1.3 71.7 - - - +
112A VAL* 1.3 60.4 + - - +
113A VAL* 3.6 8.3 - - - +
127A LEU* 3.4 2.6 - - - -
128A ASN* 2.8 66.5 + - + +
130A GLU* 5.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 3.5 34.5 - - + +
86A LEU* 4.5 5.4 - - + -
90A GLU 5.0 3.4 - - - +
91A GLU* 3.4 9.4 - - - +
92A ARG* 2.8 51.2 + - + +
110A VAL* 4.2 2.5 - - + +
111A ASP* 1.3 70.3 - - - +
113A VAL* 1.3 63.4 + - - +
114A PRO* 4.1 1.6 - - + -
125A PHE* 3.4 35.7 - - + -
126A ILE 3.4 3.6 - - - -
127A LEU* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 4.0 19.5 - - - +
111A ASP* 3.6 11.9 - - - +
112A VAL* 1.3 74.8 - - - +
114A PRO* 1.3 72.3 - - + +
115A VAL* 3.6 2.3 + - + +
125A PHE* 3.8 0.3 - - - -
126A ILE* 2.7 55.0 + - + +
128A ASN* 3.4 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA 3.4 28.5 - - - +
90A GLU* 3.7 13.0 - - - +
91A GLU* 3.7 22.4 - - + +
112A VAL* 3.8 3.8 - - + +
113A VAL* 1.3 89.2 - - + +
115A VAL* 1.3 61.8 + - - +
116A LYS* 4.0 5.3 + - + +
122A VAL* 3.7 19.1 - - + -
124A MET 4.0 4.7 - - - +
125A PHE* 4.0 13.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 6.0 0.4 - - + -
113A VAL* 4.2 3.6 - - + +
114A PRO* 1.3 73.9 - - - +
116A LYS* 1.3 69.6 + - - +
122A VAL* 3.5 2.8 - - - +
123A ILE* 3.1 28.4 + - + +
124A MET* 2.8 47.2 + - + +
126A ILE* 3.6 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA* 4.8 21.5 + - - +
114A PRO* 4.0 5.8 + - + +
115A VAL* 1.3 85.6 - - - +
117A ASN* 1.3 66.8 + - - +
120A GLY* 3.1 29.7 + - - +
121A ALA* 3.2 13.5 - - - +
122A VAL* 3.9 15.5 - - + +
123A ILE* 3.6 2.8 - - - +
----------------------------------------------------------
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