Contacts of the strand formed by residues 114 - 124 (chain A) in PDB entry 3BX9
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 114 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 3.8 38.6 - - + -
12A LYS* 4.0 24.0 - - + -
110A LEU* 3.4 5.6 - - - +
111A GLN 3.0 33.6 + - - +
112A ASP* 3.2 4.4 - - + +
113A GLY* 1.3 78.5 - - - +
115A LEU* 1.3 76.1 + - - +
116A ILE* 3.5 9.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.6 5.4 - - + -
9A MET* 4.1 20.6 - - + -
10A HIS 3.0 13.2 + - - +
11A MET* 3.3 9.3 - - + -
12A LYS 2.8 27.9 + - - -
68A THR* 4.3 14.4 - - + +
69A PHE* 3.4 39.9 - - + -
84A PHE* 3.7 36.6 - - + -
108A THR* 4.5 5.2 - - + -
109A SER 3.6 5.6 - - - +
110A LEU* 4.0 9.6 - - + +
113A GLY 4.2 0.6 + - - -
114A CYS* 1.3 76.2 - - - +
116A ILE* 1.3 59.8 + - - +
117A TYR* 4.0 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 3.4 26.7 - - + +
14A TYR* 4.3 20.6 - - + +
107A ASP* 3.4 4.9 - - - +
108A THR* 3.4 1.9 - - - -
109A SER* 2.9 48.1 + - - +
111A GLN* 4.0 31.4 - - + +
114A CYS* 3.7 22.7 - - + +
115A LEU* 1.3 82.5 - - - +
117A TYR* 1.3 69.0 + - - +
118A ASN* 5.2 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A MET* 3.6 13.5 - - + +
12A LYS 2.9 12.1 + - - -
13A LEU* 3.3 21.2 - - + -
14A TYR* 2.9 31.4 + - - -
41A MET* 3.6 21.1 - - + -
62A PHE 3.8 13.7 - - - -
63A NRQ 4.6 0.2 - - - -
66A SER* 2.6 42.3 + - - -
68A THR* 4.9 2.8 + - - -
69A PHE* 3.4 17.7 - - - -
88A PHE* 5.9 0.4 - + - -
106A GLN* 3.4 22.4 - - - +
107A ASP 3.3 3.1 - - - -
108A THR* 3.5 26.0 - - + -
115A LEU* 4.0 15.4 - - + +
116A ILE* 1.3 82.6 - - - +
118A ASN* 1.3 62.0 + - - +
119A VAL* 4.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.4 31.5 - - - +
105A THR 3.8 1.0 - - - +
106A GLN* 3.3 3.9 - - - -
107A ASP* 2.9 42.0 + - + +
116A ILE* 4.2 4.2 + - + +
117A TYR* 1.3 73.1 - - - +
119A VAL* 1.3 64.7 + - - +
120A LYS* 4.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.6 24.9 - - + -
14A TYR 2.8 14.6 + - - +
15A MET* 3.3 12.9 - - + +
16A GLU 2.9 26.0 + - - -
61A SER* 3.6 29.8 - - - +
90A TRP* 4.3 6.3 - - + -
104A ALA* 4.7 0.2 - - + -
105A THR 3.5 9.2 - - - +
106A GLN* 3.9 14.8 - - + -
117A TYR* 4.7 0.4 - - + -
118A ASN* 1.3 81.0 + - - +
120A LYS* 1.3 67.6 + - - +
121A ILE* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.2 12.1 - - + +
104A ALA* 3.2 5.4 - - - -
105A THR* 2.9 45.8 + - - +
118A ASN* 4.2 20.7 + - - +
119A VAL* 1.3 78.5 - - - +
121A ILE* 1.3 63.5 + - - +
122B ARG* 5.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MET* 4.2 28.3 - - + -
16A GLU 2.9 10.5 + - - +
17A GLY* 3.1 19.1 - - - -
18A THR 3.1 4.7 + - - -
19A VAL* 4.3 7.0 - - + -
24A PHE* 4.1 19.5 - - + -
58A LEU* 4.1 7.2 - - + -
61A SER* 3.4 17.0 - - - +
102A LEU* 3.9 29.2 - - + -
103A THR 3.5 1.1 - - - -
104A ALA* 3.3 29.8 - - + -
119A VAL* 3.7 11.2 - - + -
120A LYS* 1.3 80.1 - - - +
122A ARG* 1.3 69.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.4 42.7 + - - +
20A ASN 5.4 0.4 - - - +
21A ASN* 4.6 3.4 + - - +
101A VAL 3.8 1.2 - - - +
102A LEU* 3.5 1.8 - - - -
103A THR* 2.7 50.0 + - - +
121A ILE* 1.3 78.1 + - - +
123A GLY* 1.3 67.0 + - - +
124A VAL* 3.6 28.3 + - + +
91B GLU* 3.2 26.3 + - - +
103B THR* 5.2 11.2 - - + +
105B THR* 3.2 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR 3.0 9.2 + - - -
19A VAL* 3.3 9.8 - - - +
20A ASN 2.8 27.4 + - - -
101A VAL 3.1 9.0 - - - -
102A LEU* 4.1 7.6 - - - -
121A ILE* 4.2 1.0 - - - +
122A ARG* 1.3 78.6 + - - +
124A VAL* 1.3 66.2 + - - +
126A PHE* 3.8 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 3.8 4.5 - - - +
101A VAL* 2.8 44.6 + - + +
122A ARG* 3.6 28.0 - - + +
123A GLY* 1.3 79.5 - - - +
125A ASN* 1.3 79.0 + - - +
126A PHE* 3.3 4.8 + - - -
91B GLU* 3.9 24.2 - - + +
92B ARG 5.1 3.4 - - - +
93B VAL* 3.9 26.7 - - + +
103B THR* 5.7 3.8 - - + -
105B THR* 5.4 0.4 - - + -
175B LYS 5.7 0.2 - - - +
177B THR* 5.3 4.7 - - - +
----------------------------------------------------------
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