Contacts of the helix formed by residues 87 - 96 (chain A) in PDB entry 2BT4
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 SER 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 2.5 29.2 + - - -
83A TYR* 2.8 37.7 + - - +
86A THR* 1.3 68.9 + - - +
88A VAL* 1.3 61.3 + - - +
89A ALA 3.5 0.2 + - - -
90A ILE* 3.0 33.6 + - - +
91A LEU 3.4 12.0 + - - -
121A TYR* 3.9 15.0 - - - +
122A VAL* 5.2 1.6 - - - +
2405A TRS 3.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 4.8 0.2 + - - -
86A THR 3.3 4.8 + - - -
87A SER* 1.3 72.5 - - - +
89A ALA* 1.3 58.4 + - - +
91A LEU* 3.2 7.1 + - + +
92A ASP* 2.8 29.1 + - - +
121A TYR* 3.5 39.3 - - + +
482C ALA* 3.6 15.0 - - + +
485C HIS* 4.3 10.3 - - + -
486C THR* 3.9 21.9 - - + +
516C PHE* 3.5 30.1 - - + -
517C ARG* 3.9 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.9 1.7 + - - +
63A VAL* 3.9 9.6 - - + +
87A SER* 3.1 7.3 + - - +
88A VAL* 1.3 78.1 - - - +
90A ILE* 1.3 57.1 + - - +
93A ALA* 3.0 23.9 + - - +
415C PRO* 3.9 14.1 - - + -
416C ASN* 3.1 12.9 + - - +
482C ALA* 3.3 18.5 - - + +
483C TYR* 3.7 33.6 - - + +
486C THR* 5.5 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 4.1 6.3 - - + -
62A LEU* 4.0 30.7 - - + -
63A VAL* 3.9 17.3 - - + -
66A ILE* 4.0 15.5 - - + -
78A ILE* 4.2 10.5 - - + -
80A PRO* 5.1 4.0 - - + -
83A TYR* 3.7 27.1 - - + -
87A SER* 3.0 24.4 + - - +
89A ALA* 1.3 71.3 - - - +
91A LEU* 1.3 67.4 + - - +
93A ALA* 3.0 7.7 + - - +
94A LEU* 2.9 29.7 + - + +
122A VAL* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER 3.4 10.7 + - - +
88A VAL* 3.2 10.4 + - + +
90A ILE* 1.3 76.5 - - - +
92A ASP* 1.3 60.2 + - - +
94A LEU* 3.0 10.0 + - - +
95A ASN* 2.8 37.5 + - - +
121A TYR* 3.4 37.7 - - + +
122A VAL* 4.6 4.2 - - - +
124A GLN* 3.7 24.0 - - + +
125A ARG* 3.6 30.1 - - + +
516C PHE* 3.8 20.0 - - + -
517C ARG* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 2.8 21.6 + - - +
89A ALA 4.2 0.4 - - - -
91A LEU* 1.3 73.7 - - - +
93A ALA* 1.3 61.6 + - - +
95A ASN* 3.2 15.9 + - - +
96A THR* 3.3 17.7 + - - +
416C ASN* 3.2 22.3 + - + +
482C ALA* 3.4 12.7 + - - +
517C ARG* 2.9 33.1 + - - -
560C CA2 2.5 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 4.2 11.2 - - + -
66A ILE* 3.5 36.3 - - + +
67A HIS* 4.2 2.2 - - - +
89A ALA 3.0 13.3 + - - +
90A ILE* 3.0 9.4 + - - +
92A ASP* 1.3 74.2 - - - +
94A LEU* 1.3 62.1 + - - +
96A THR* 2.6 27.0 + - - -
97A CYS* 3.7 1.0 - - - -
416C ASN* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 4.0 19.1 - - + -
76A ILE* 3.9 32.3 - - + -
78A ILE* 4.7 6.5 - - + -
90A ILE* 2.9 28.1 + - + +
91A LEU* 3.5 6.7 - - - +
93A ALA* 1.3 76.7 - - - +
95A ASN* 1.3 58.8 + - - +
97A CYS* 2.9 27.0 + - - +
102A VAL* 4.1 22.6 - - + +
122A VAL* 3.8 31.9 - - + +
125A ARG* 3.4 28.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 2.8 31.7 + - - +
92A ASP* 3.4 12.6 + - - +
93A ALA 3.2 0.2 - - - -
94A LEU* 1.3 77.7 - - - +
96A THR* 1.3 57.9 + - - +
97A CYS 3.2 1.4 + - - -
98A ASP* 4.1 3.6 + - - -
124A GLN 5.3 0.2 - - - +
125A ARG* 3.4 33.0 + - - +
423C ARG* 3.0 35.8 + - - +
517C ARG* 4.0 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 4.3 3.6 - - - -
70A ARG* 2.8 41.5 + - - -
92A ASP 3.3 15.0 + - - +
93A ALA* 2.6 21.9 + - - +
95A ASN* 1.3 76.9 - - - +
97A CYS* 1.3 57.3 + - - +
98A ASP* 3.1 16.5 + - - +
416C ASN* 4.6 6.5 - - + +
419C LEU* 3.8 20.7 - - + +
423C ARG* 3.6 13.4 - - - +
560C CA2 4.4 24.0 - - + -
----------------------------------------------------------
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