Contacts of the helix formed by residues 102 - 115 (chain A) in PDB entry 5B82
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 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 1.3 89.4 - - + +
103A ALA* 1.3 64.1 + - - +
104A LEU* 3.5 11.3 + - - +
105A ASP* 3.1 35.6 + - - +
106A VAL* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 1.3 73.8 - - - +
104A LEU* 1.3 57.1 + - - +
106A VAL* 3.4 8.3 + - - +
107A GLN* 2.9 31.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
102A THR* 3.1 10.8 + - - +
103A ALA* 1.3 76.7 - - - +
105A ASP* 1.3 67.3 + - - +
107A GLN* 3.7 16.8 - - - +
108A ALA* 2.9 23.1 + - + +
121A PHE* 5.4 0.4 - - + -
123A GLN* 3.4 31.4 - - - +
125A ASP* 4.0 10.8 - - - +
130A HIS* 3.8 32.8 - - + +
132A PHE* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.0 20.9 + - - -
89A VAL* 4.2 9.2 - - + +
100A PRO* 4.0 10.8 - - + -
101A ARG* 2.9 29.7 + - - +
102A THR* 3.1 22.5 + - - +
104A LEU* 1.3 77.3 - - - +
106A VAL* 1.3 57.8 + - - +
108A ALA 3.2 1.0 + - - -
109A LEU* 3.0 36.0 + - - +
132A PHE* 4.3 8.5 - - - -
175A MET* 3.6 20.5 - - + +
177A ALA* 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PRO* 4.3 17.9 - - + -
102A THR 3.3 13.8 + - - +
103A ALA* 3.8 9.4 - - - +
104A LEU 3.2 0.4 - - - -
105A ASP* 1.3 76.3 - - - +
107A GLN* 1.3 57.2 + - - +
109A LEU* 3.5 7.6 + - - +
110A ASN* 2.9 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 2.9 16.8 + - - +
104A LEU* 3.6 25.8 - - - +
106A VAL* 1.3 78.4 - - - +
108A ALA* 1.3 55.7 + - - +
110A ASN* 3.4 9.7 + - - +
111A GLN* 2.9 44.3 + - + +
123A GLN* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 2.9 17.9 + - + +
105A ASP 3.2 3.6 + - - +
107A GLN* 1.3 73.1 - - - +
109A LEU* 1.3 67.4 + - - +
111A GLN* 3.0 5.2 + - - +
112A PHE* 3.0 29.0 + - - -
121A PHE* 3.7 31.2 - - + -
132A PHE* 3.8 14.6 - - + -
175A MET* 3.7 18.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
89A VAL* 4.2 10.1 - - + +
90A ALA* 4.5 0.9 - - - -
91A LEU* 4.1 20.0 - - + +
100A PRO* 4.0 27.4 - - + -
105A ASP 3.0 21.9 + - - +
106A VAL* 3.8 6.7 - - - +
108A ALA* 1.3 76.0 - - - +
110A ASN* 1.3 58.0 + - - +
112A PHE* 3.3 7.2 + - + +
113A ASP* 2.9 30.1 + - - +
172A LEU* 3.8 14.0 - - + +
174A GLY* 4.2 22.4 - - - +
175A MET* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 2.9 39.5 + - - +
107A GLN* 3.4 7.9 - - - +
108A ALA 3.2 0.2 - - - -
109A LEU* 1.3 76.1 - - - +
111A GLN* 1.3 57.7 + - - +
113A ASP* 3.2 10.2 + - - +
114A ASN* 2.9 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLN* 2.9 41.4 + - + +
108A ALA 3.0 8.9 + - - +
110A ASN* 1.3 74.2 - - - +
112A PHE* 1.3 65.0 + - - +
114A ASN* 3.3 5.2 + - - +
115A ASN* 3.1 25.6 + - - +
118A LEU* 3.8 18.4 - - + +
121A PHE* 3.5 41.0 - - + +
123A GLN* 4.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA 3.0 23.5 + - - -
109A LEU* 3.6 8.3 - - + +
111A GLN* 1.3 75.3 - - - +
113A ASP* 1.3 62.3 + - - +
114A ASN 3.2 0.2 + - - -
115A ASN 3.2 11.3 + - - +
116A HIS* 4.0 0.3 + - - -
118A LEU* 3.5 29.2 - - + -
119A GLN 3.5 24.2 - - - -
120A ALA* 3.8 3.8 - - - -
121A PHE* 3.9 7.6 - + - -
132A PHE* 3.6 38.8 - - + -
134A ARG* 3.0 58.6 + - + +
172A LEU* 4.0 14.8 - - + -
175A MET* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU 2.9 18.9 + - - +
110A ASN* 3.6 11.9 - - - +
112A PHE* 1.3 77.0 - - - +
114A ASN* 1.3 69.2 + - - +
115A ASN 3.7 0.2 + - - -
116A HIS* 5.0 2.6 + - - +
134A ARG* 4.9 2.2 + - - +
172A LEU* 3.8 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN* 2.9 33.7 + - - +
111A GLN* 4.1 4.0 - - - +
113A ASP* 1.3 87.6 - - - +
115A ASN* 1.3 60.4 + - - +
116A HIS 4.1 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN 3.1 12.7 + - - +
112A PHE 3.2 3.7 + - - +
114A ASN* 1.3 79.9 - - - +
116A HIS* 1.3 57.7 + - - +
117A HIS* 3.2 24.0 + - - +
118A LEU* 2.9 44.5 + - + +
134A ARG* 3.0 12.1 + - - -
----------------------------------------------------------
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