Contacts of the helix formed by residues 65 - 84 (chain A) in PDB entry 2KSB
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 65 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.0 21.5 - - - +
64A ARG* 1.3 80.9 - - - +
66A VAL* 1.3 64.0 + - - +
67A THR* 3.3 9.7 + - - -
68A ASN* 2.8 44.4 + - - +
69A TYR* 2.7 21.7 + - - -
243A LYS* 5.7 7.2 - - - +
311A ARG* 4.4 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 1.3 73.2 - - - +
67A THR* 1.3 76.6 + - - +
69A TYR* 2.8 36.8 + - - +
70A PHE* 3.0 31.5 - - + -
129A ASP* 5.2 8.5 - - + -
130A ARG* 6.2 1.1 - - - +
142A LEU* 4.5 29.8 - - + -
144A ALA* 5.9 0.7 - - - -
147A THR* 2.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 3.1 9.2 + - - -
66A VAL* 1.3 90.6 - - - +
68A ASN* 1.3 61.6 + - - +
70A PHE* 2.9 20.3 + - + +
71A LEU* 2.8 41.5 + - + +
126A VAL* 4.9 4.3 - - + -
129A ASP* 4.1 3.3 + - - -
130A ARG* 3.2 23.6 + - - -
246A VAL* 4.8 3.8 - - + +
250A MET* 2.9 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.3 18.2 - - + +
62A ARG* 5.2 0.2 - - - +
63A MET* 2.8 55.3 + - - +
64A ARG* 4.7 3.1 - - - +
65A THR* 2.8 36.4 + - - +
67A THR* 1.3 78.6 - - - +
69A TYR* 1.3 62.5 + - + +
71A LEU* 3.4 9.1 + - - +
72A VAL* 3.0 28.2 + - - +
311A ARG* 5.6 1.2 - - - +
312A PHE* 4.0 16.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 4.4 29.3 + - + +
65A THR 2.7 34.1 - - - -
66A VAL* 2.8 21.9 + - + +
68A ASN* 1.3 78.6 - - + +
70A PHE* 1.3 56.8 + - - +
72A VAL* 2.7 34.7 - - + +
73A ASN* 3.3 4.0 + - - +
144A ALA* 3.9 25.1 - - + +
147A THR* 3.4 22.4 - - + -
148A LYS* 3.7 28.1 - - + -
151A ILE* 4.4 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 3.0 44.6 - - + -
67A THR* 2.9 14.4 + - - +
69A TYR* 1.3 75.4 - - - +
71A LEU* 1.3 53.0 + - + +
73A ASN* 3.0 17.2 + - - +
74A LEU* 2.7 25.2 - - - +
122A SER* 4.3 3.8 - - - +
125A ALA* 4.3 16.4 - - + -
126A VAL* 4.0 20.9 - - + -
129A ASP* 3.7 25.8 - - + -
147A THR* 3.1 26.9 - - + -
150A VAL* 4.2 22.0 - - + -
151A ILE* 3.1 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 5.2 2.2 - - + -
57A ILE* 4.9 5.2 - - + -
67A THR* 2.8 51.4 + - + +
68A ASN* 3.7 14.6 - - - +
70A PHE* 1.3 77.1 - - + +
72A VAL* 1.3 64.6 + - - +
74A LEU* 3.1 16.0 + - + +
75A ALA* 2.8 22.7 + - - +
123A MET* 6.2 0.2 - - + -
126A VAL* 5.1 7.4 - - + -
249A MET* 4.6 5.6 - - + -
250A MET* 4.8 4.5 - - + -
305A TYR* 2.9 47.7 + - + +
312A PHE* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 5.6 0.2 - - - -
54A MET* 5.2 6.8 - - + +
57A ILE* 2.9 38.1 - - + -
58A LEU* 4.1 15.7 - - + -
64A ARG* 5.5 1.8 - - - +
68A ASN 3.0 9.1 + - - +
69A TYR* 2.7 28.7 - - + +
71A LEU* 1.3 75.3 - - - +
73A ASN* 1.3 56.0 + - + +
75A ALA* 3.0 8.9 + - - +
76A PHE* 2.7 36.6 + - - +
151A ILE* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR 4.1 0.9 - - - +
70A PHE 3.0 14.3 + - - +
72A VAL* 1.3 84.4 - - + +
74A LEU* 1.3 58.8 + - - +
76A PHE* 3.2 7.6 + - - +
77A ALA* 3.0 22.1 + - - +
118A ALA* 4.8 4.4 + - - +
122A SER* 3.9 17.1 + - - +
151A ILE* 3.2 39.2 - - + +
154A ILE* 3.6 21.2 - - - +
155A TRP* 2.7 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 2.7 40.6 + - + +
71A LEU* 3.4 14.1 - - + +
73A ASN* 1.3 77.5 - - - +
75A ALA* 1.3 58.1 + - - +
77A ALA* 3.0 6.3 + - - +
78A GLU* 2.6 46.4 + - - +
119A SER* 5.3 9.4 - - - +
122A SER* 2.9 29.6 - - - +
123A MET* 3.1 37.0 - - + -
126A VAL* 4.7 0.9 - - + -
253A VAL* 4.4 10.8 - - + -
301A ASN* 4.8 7.6 - - + +
305A TYR* 5.0 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 3.8 38.6 + - - +
53A VAL* 4.3 15.7 - - + -
54A MET* 4.6 7.6 - - + +
71A LEU 2.8 14.1 + - - +
72A VAL* 3.3 11.7 - - - +
74A LEU* 1.3 75.5 - - - +
76A PHE* 1.3 58.2 + - - +
78A GLU* 3.1 5.6 + - - +
79A ALA* 2.9 27.6 + - - +
301A ASN* 4.5 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET* 6.0 0.6 - - - +
72A VAL* 2.7 16.7 + - + +
73A ASN* 3.4 13.0 - - - +
75A ALA* 1.3 71.3 - - - +
77A ALA* 1.3 64.0 + - - +
79A ALA* 3.0 13.9 + - + +
80A SER* 3.0 31.8 + - - -
84A PHE* 6.1 3.4 - + - -
155A TRP* 3.4 39.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.0 13.7 + - - +
74A LEU* 3.0 6.3 + - - +
76A PHE* 1.3 81.1 - - - +
78A GLU* 1.3 73.6 + - - +
80A SER* 3.4 8.2 + - - +
81A MET* 3.3 17.4 + - - +
115A ALA* 4.2 24.6 - - + +
118A ALA* 4.9 5.4 - - + -
119A SER* 4.0 15.0 - - - +
155A TRP* 4.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 3.2 21.5 - - - +
74A LEU* 2.6 39.9 + - - +
75A ALA 3.1 1.3 + - - +
77A ALA* 1.3 83.0 - - - +
79A ALA* 1.3 64.7 + - - +
81A MET* 3.0 7.8 + - + +
82A ALA* 2.9 19.4 + - - +
119A SER* 3.8 11.2 + - - -
297A SER 4.9 0.7 - - - +
298A THR* 3.1 50.2 + - - +
300A TYR* 6.6 0.4 - - - -
301A ASN* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER 5.6 0.2 - - - -
47A VAL* 6.0 1.3 - - - +
50A ASN* 4.5 11.4 - - + +
51A VAL* 6.1 0.4 - - - +
54A MET* 5.8 8.3 - - - -
75A ALA 2.9 12.9 + - - +
76A PHE* 3.0 19.4 + - + +
78A GLU* 1.3 73.4 - - - +
80A SER* 1.3 55.5 + - - +
82A ALA* 3.0 7.4 + - - +
83A ALA* 2.7 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 3.0 27.3 + - - -
77A ALA* 3.7 9.6 - - - -
78A GLU 3.2 0.2 - - - -
79A ALA* 1.3 75.8 - - - +
81A MET* 1.3 57.4 + - - +
83A ALA* 4.8 0.2 - - - -
84A PHE* 2.6 64.6 + - - +
85A ASN* 4.4 0.4 - - - -
111A PHE* 4.9 15.1 + - - +
115A ALA* 5.5 5.8 - - - -
155A TRP* 5.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.6 0.7 - - - +
77A ALA 3.3 8.4 + - - +
78A GLU* 3.0 13.6 + - + +
80A SER* 1.3 78.0 - - - +
82A ALA* 1.3 59.4 + - - +
85A ASN* 2.7 43.3 + - - +
86A THR* 2.7 31.5 + - - -
112A PRO* 5.7 1.1 - - + +
115A ALA* 4.8 16.1 - - + +
116A VAL* 5.3 2.7 - - + -
261A TRP* 4.6 13.9 - - + +
294A ALA 4.5 5.6 - - - +
295A MET* 3.2 36.3 - - - +
297A SER* 5.7 1.1 - - - -
298A THR* 3.2 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 6.3 0.2 - - - -
43A VAL* 4.1 8.0 - - - +
46A SER* 3.6 26.7 - - - -
47A VAL* 3.3 32.0 - - + +
78A GLU 2.9 9.5 + - - +
79A ALA* 3.7 7.6 - - - +
81A MET* 1.3 78.5 - - - +
83A ALA* 1.3 59.1 + - - +
86A THR* 2.7 30.4 - - - +
87A VAL* 3.9 2.9 - - - +
298A THR* 4.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.9 3.1 - - + +
79A ALA* 2.7 20.9 + - + +
82A ALA* 1.3 75.0 - - - +
84A PHE* 1.4 74.1 + - + +
87A VAL* 2.7 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 6.1 3.8 - + - -
80A SER* 2.6 44.3 + - - +
83A ALA* 1.4 88.0 - - + +
85A ASN* 1.4 68.1 + - + +
87A VAL* 4.0 0.7 - - - +
88A VAL* 3.5 24.3 + - - +
108A HIS* 4.9 2.1 - - - -
111A PHE* 5.0 30.1 - + + -
----------------------------------------------------------
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