Contacts of the helix formed by residues 55 - 75 (chain b) in PDB entry 5XTD
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 55 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51b LEU* 3.7 9.9 + - - +
54b LYS* 1.3 90.2 - - - +
56b PRO* 1.3 76.0 - - - +
57b TRP* 3.1 24.2 + - - +
58b ARG* 3.4 17.5 + - - +
59b LYS* 3.7 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 56 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54b LYS 4.5 2.5 - - - +
55b SER* 1.3 87.2 - - - +
57b TRP* 1.3 60.8 + - + +
58b ARG 3.2 0.2 - - - -
59b LYS* 2.8 45.6 + - + +
60b MET* 3.0 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 57 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55b SER* 3.1 15.7 + - - +
56b PRO* 1.3 80.5 - - + +
58b ARG* 1.3 77.0 + - - +
60b MET* 3.5 27.5 + - + +
61b VAL* 3.9 13.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47b TRP* 5.8 5.1 - - + -
50b PHE* 3.1 52.2 + - + +
51b LEU* 3.5 8.8 - - + +
54b LYS* 4.6 21.6 - - + +
55b SER* 3.4 10.9 + - - +
56b PRO 3.2 0.6 - - - -
57b TRP* 1.3 88.9 - - - +
59b LYS* 1.3 60.0 - - - +
61b VAL* 3.0 26.9 - - - +
62b HIS 3.0 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51b LEU* 3.4 21.8 - - + +
55b SER 3.7 2.6 + - - +
56b PRO* 2.8 38.4 + - + +
58b ARG* 1.3 78.0 - - - +
60b MET* 1.3 63.6 + - - +
62b HIS* 3.0 16.1 + - + +
63b GLY* 3.0 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56b PRO 3.0 9.2 + - - +
57b TRP* 3.6 25.6 - - + +
58b ARG 3.2 0.4 - - - -
59b LYS* 1.3 78.8 - - - +
61b VAL* 1.3 63.9 + - + +
63b GLY* 3.9 1.7 + - - -
64b VAL* 3.7 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47b TRP* 4.2 11.3 - - + -
57b TRP* 4.3 12.6 - - + +
58b ARG* 3.0 42.8 - - - +
60b MET* 1.3 80.2 - - + +
62b HIS* 1.3 61.0 + - - +
63b GLY 3.2 1.6 - - - -
64b VAL* 3.1 16.6 - - + +
65b TYR* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47b TRP* 2.9 40.2 - + + +
48b ASN* 4.1 6.7 + - - -
51b LEU* 3.3 45.0 - - + +
58b ARG 3.0 6.1 + - - -
59b LYS* 3.0 14.0 + - + +
61b VAL* 1.3 78.8 - - - +
63b GLY* 1.3 64.7 + - - +
65b TYR* 3.1 4.2 + - - +
66b LYS* 2.9 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59b LYS 3.0 13.2 + - - -
60b MET 3.9 2.7 + - - -
61b VAL 3.2 0.2 - - - -
62b HIS* 1.3 82.9 + - - +
64b VAL* 1.3 55.9 + - - +
66b LYS* 3.2 6.3 + - - +
67b LYS* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60b MET 3.7 7.5 + - - +
61b VAL* 3.1 34.5 - - + +
63b GLY* 1.3 72.6 - - - +
65b TYR* 1.3 60.9 + - - +
67b LYS* 3.8 11.8 - - + +
68b SER* 2.9 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47b TRP* 3.6 35.7 - + + -
61b VAL 2.9 15.1 + - - +
62b HIS 3.2 7.2 - - - +
63b GLY 3.1 0.2 - - - -
64b VAL* 1.3 77.4 - - - +
66b LYS* 1.3 99.3 + - + +
68b SER* 2.9 16.9 + - - -
69b ILE* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47b TRP* 3.3 12.7 - - - +
48b ASN* 5.2 1.2 + - - -
62b HIS* 2.9 55.3 + - + +
63b GLY* 3.2 7.6 + - - +
65b TYR* 1.3 103.3 - - + +
67b LYS* 1.3 64.4 + - + +
69b ILE* 3.4 11.8 - - + +
70b PHE* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63b GLY 2.9 25.1 + - - +
64b VAL* 3.8 11.0 - - + +
66b LYS* 1.3 76.9 - - + +
68b SER* 1.3 57.4 + - - +
70b PHE* 3.6 7.7 + - - +
71b VAL* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64b VAL* 2.9 20.5 + - - -
65b TYR* 2.9 9.8 + - - -
67b LYS* 1.3 76.1 - - - +
69b ILE* 1.3 61.4 + - - +
71b VAL* 3.1 8.2 + - - +
72b PHE* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65b TYR* 2.9 39.7 + - + +
66b LYS* 3.4 20.4 - - + +
68b SER* 1.3 76.7 - - - +
70b PHE* 1.3 61.0 + - - +
72b PHE* 3.3 16.1 + - + +
73b THR* 2.9 45.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66b LYS 3.0 20.2 + - - +
67b LYS* 3.6 9.9 - - - +
69b ILE* 1.3 79.9 - - + +
71b VAL* 1.3 68.5 + - + +
73b THR* 3.3 4.0 + - - -
74b HIS* 2.9 80.1 + + + +
75b VAL* 5.3 4.9 - - + -
35l TYR* 4.6 7.0 - + - -
38l SER* 4.8 9.4 - - - -
39l ILE* 4.1 20.0 - - + -
42l SER* 3.9 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67b LYS* 3.0 24.9 + - + +
68b SER* 3.1 8.0 + - - +
70b PHE* 1.3 86.7 - - + +
72b PHE* 1.3 62.8 + - - +
75b VAL* 3.1 36.4 - - + +
76b LEU* 3.3 12.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68b SER 2.9 12.9 + - - +
69b ILE* 3.7 19.5 - - + +
70b PHE 3.2 0.2 - - - -
71b VAL* 1.3 81.4 - - - +
73b THR* 1.3 75.9 + - + +
76b LEU* 3.3 33.7 + - + +
77b VAL* 3.3 32.0 + - + +
80b TRP* 4.1 26.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69b ILE* 2.9 35.5 + - + +
70b PHE* 3.7 1.2 - - - -
72b PHE* 1.3 91.1 - - + +
74b HIS* 1.3 93.5 + - - +
77b VAL* 4.0 7.7 - - - +
78b PRO* 3.3 18.5 - - - +
502r PLX 5.4 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 74 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70b PHE* 2.9 51.5 + + + +
73b THR* 1.3 105.6 + - - +
75b VAL* 1.3 64.6 + - + +
78b PRO* 3.8 13.1 - - - +
10l LEU* 5.7 1.6 - - - +
14l SER* 4.8 14.0 - - - -
17l PRO* 4.4 23.3 - - + +
35l TYR* 2.4 34.3 + + - -
39l ILE* 4.2 12.1 - - + -
502r PLX 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70b PHE* 4.7 6.7 - - + +
71b VAL* 3.1 32.1 + - + +
73b THR 3.2 1.4 - - - -
74b HIS* 1.3 88.8 - - + +
76b LEU* 1.3 76.7 + - + +
77b VAL 3.4 1.6 - - - -
78b PRO* 3.1 8.3 - - - +
79b VAL* 3.0 32.3 + - + +
10l LEU* 4.4 10.2 - - + +
42l SER* 5.8 5.6 - - - +
46l ILE* 4.7 26.5 - - + -
----------------------------------------------------------
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