Contacts of the strand formed by residues 32 - 43 (chain A) in PDB entry 5TKM
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 TYR 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 4.2 12.0 + - - +
30A ARG* 3.2 3.4 - - - +
31A SER* 1.3 90.4 - - - +
33A THR* 1.3 60.3 + - - +
34A TRP* 4.1 11.0 - - + +
56A ARG* 3.5 58.5 + - + -
57A GLY 3.2 20.2 - - - +
58A GLN* 3.4 29.0 + - - -
59A VAL* 3.3 6.3 - - - -
93A SER* 3.9 3.3 + - - -
94A TRP* 3.3 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 1.3 72.3 - - - +
34A TRP* 1.3 72.4 + - - +
35A LEU* 5.0 1.1 - - + -
56A ARG* 3.4 3.3 - - - +
57A GLY 2.9 32.6 + - - +
58A GLN 4.4 5.3 + - - -
59A VAL* 3.2 24.6 - - - +
67A ALA* 3.6 22.2 - - + +
68A GLU* 4.1 14.1 + - - +
92A VAL* 4.7 4.3 - - + -
93A SER* 3.5 7.9 - - - +
94A TRP* 3.4 31.0 - - - +
95A THR 5.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A MET* 3.9 29.2 - - + -
12A MET* 4.0 15.3 - - + -
16A THR* 3.5 24.9 - - + -
20A ASN* 3.4 39.0 + - + +
21A PHE* 3.7 24.2 - + + -
32A TYR* 4.1 7.5 - - + +
33A THR* 1.3 78.8 - - - +
35A LEU* 1.3 59.4 + - - +
36A CYS 4.1 0.4 - - - -
54A VAL* 3.4 32.1 - - + -
55A PHE 3.5 7.4 - - - -
56A ARG* 3.3 45.3 - - + +
91A PHE 3.7 0.9 - - - +
92A VAL* 3.3 4.9 - - - -
93A SER* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 5.0 0.9 - - + -
34A TRP* 1.3 74.3 - - - +
36A CYS* 1.3 61.6 + - - +
37A TYR* 3.9 15.5 + - + -
54A VAL* 3.3 3.7 - - - +
55A PHE* 2.8 44.2 + - + +
67A ALA* 3.9 31.4 - - + +
68A GLU* 4.0 7.6 - - + +
71A PHE* 4.2 10.3 - - + -
90A TRP* 3.6 60.6 - - + +
91A PHE 3.7 2.5 - - - -
92A VAL* 3.6 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MET* 3.5 32.3 - - - -
21A PHE* 4.2 9.0 - - - -
35A LEU* 1.3 75.7 - - - +
37A TYR* 1.3 60.4 + - - +
53A GLY 3.5 5.2 - - - -
54A VAL* 4.1 3.8 - - - +
89A THR 3.7 0.3 - - - +
90A TRP* 3.2 4.7 - - - -
91A PHE* 2.7 52.6 + - + +
156A CYS* 4.7 4.5 - - - -
160A PHE* 3.6 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 3.2 24.7 - - + +
35A LEU* 3.9 4.9 - - + -
36A CYS* 1.3 75.2 - - - +
38A GLU* 1.3 65.0 + - - +
39A VAL* 4.0 10.1 - - + -
51A ASP* 4.2 2.0 + - - -
52A THR* 3.3 41.8 + - - -
53A GLY 3.0 40.7 + - - -
54A VAL 3.7 1.1 - - - -
55A PHE* 3.3 33.2 - + - -
71A PHE* 3.5 27.8 - + + -
74A TRP* 3.6 32.8 - + - -
89A THR 3.2 8.5 - - - +
90A TRP* 3.8 8.5 - - + -
91A PHE* 5.7 0.4 - - - -
160A PHE* 3.4 9.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 1.3 80.7 - - - +
39A VAL* 1.3 63.0 + - - +
40A LYS* 3.2 26.9 + - + +
49A LEU* 3.8 19.7 - - + +
51A ASP 3.4 3.8 - - - -
52A THR* 3.7 11.3 - - + +
87A GLN 3.6 1.9 - - - +
88A ILE* 3.5 4.3 - - - +
89A THR* 2.9 43.7 + - - +
91A PHE* 5.0 6.3 - - + -
155A TYR* 2.4 43.5 + - - -
159A ASN* 4.8 4.0 - - - +
160A PHE* 3.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 4.0 17.9 - - + -
38A GLU* 1.3 74.8 - - - +
40A LYS* 1.3 56.0 + - - +
49A LEU* 4.2 0.7 - - - +
50A TRP* 2.8 39.1 + - + +
51A ASP* 2.7 27.7 + - + +
71A PHE* 4.3 9.6 - - + -
74A TRP* 4.4 7.4 - - + -
75A PHE* 4.2 27.1 - - + -
79A GLN* 4.5 7.9 - - + +
86A PHE* 3.7 33.7 - - + -
87A GLN 3.8 2.9 - - - +
88A ILE* 4.6 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 3.2 31.0 + - + +
39A VAL* 1.3 78.6 - - - +
41A ILE* 1.3 65.3 + - - +
47A ASN* 2.8 43.6 + - - +
48A LEU 3.1 12.8 - - - +
49A LEU* 4.1 16.6 - - + +
86A PHE* 3.3 7.6 - - - +
87A GLN* 2.8 58.2 + - + +
89A THR* 5.7 1.6 - - - -
155A TYR* 5.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 1.3 71.7 - - - +
42A LYS* 1.3 61.8 + - - +
43A ARG* 6.1 1.8 - - + -
46A SER* 4.0 4.9 + - - +
47A ASN* 3.6 2.4 + - - -
48A LEU* 2.9 43.7 + - + +
50A TRP* 3.8 39.7 - - + +
84A LYS* 4.0 36.3 - - + +
85A CYS 3.4 9.2 - - - +
86A PHE* 3.4 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS 3.7 0.8 + - - +
41A ILE* 1.3 75.8 - - - +
43A ARG* 1.3 66.3 + - - +
44A GLY* 3.3 23.6 + - - +
46A SER 3.6 6.6 + - - +
47A ASN* 3.4 27.7 - - - +
85A CYS* 3.1 33.8 + - - +
86A PHE 5.3 0.4 - - - -
87A GLN* 3.1 48.7 - - + +
115A THR* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.3 2.2 - - + -
42A LYS* 1.3 76.7 - - - +
44A GLY* 1.3 66.1 + - - +
45A ARG 3.1 4.3 + - - -
46A SER* 3.2 30.9 + - - +
85A CYS* 5.5 5.4 - - + -
----------------------------------------------------------
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