Contacts of the helix formed by residues 41 - 56 (chain S) 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 PHE 41 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39S ALA 3.1 13.0 - - - +
40S HIS* 1.3 101.1 + + - +
42S GLY* 1.3 67.7 + - - +
43S TYR* 3.2 3.6 - - + +
44S HIS* 3.2 42.5 + + + +
45S TRP 3.5 1.0 + - - -
65W PHE* 6.3 4.3 - + - -
140W PHE* 4.2 0.2 - - - -
133m GLY 4.6 0.2 - - - +
134m PHE* 2.8 36.8 - + + +
135m ILE* 3.9 17.0 - - + -
136m ARG* 4.7 4.9 - - + -
99s ASN* 4.5 12.3 - - - -
317s GLN* 5.2 20.0 - - + -
318s THR* 4.2 25.1 - - - -
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Residues in contact with GLY 42 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S HIS 4.0 1.2 + - - -
41S PHE* 1.3 73.2 - - - +
43S TYR* 1.3 57.6 + - - +
45S TRP* 2.9 21.9 + - - +
46S SER* 2.9 13.0 + - - -
140W PHE* 4.1 16.2 - - - -
130m GLU* 4.6 8.3 - - - -
131m GLY 4.3 10.2 - - - +
132m SER* 4.2 6.5 - - - -
133m GLY 3.6 10.0 + - - -
134m PHE 4.8 0.4 + - - -
135m ILE 5.9 0.4 - - - -
136m ARG* 5.0 5.0 - - - +
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Residues in contact with TYR 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S PHE* 3.2 1.0 - - + -
42S GLY* 1.3 77.5 - - - +
44S HIS* 1.3 89.8 + + + +
46S SER* 2.6 19.7 + - - -
47S LEU* 2.9 44.5 + - + +
68W ARG* 3.4 53.8 - - + +
71W LEU* 4.0 18.6 - - + +
72W LEU* 5.0 2.0 - - + -
75W LEU* 4.2 16.8 - - + -
132m SER* 3.2 37.4 + - - +
133m GLY 3.4 11.6 + - - +
134m PHE* 4.2 9.6 - + + -
26u LYS* 5.5 5.7 - - - -
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Residues in contact with HIS 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ARG* 5.5 1.2 + - - -
38S VAL* 4.1 12.5 + - - +
39S ALA* 3.8 17.8 - - + +
40S HIS* 4.6 10.5 - + - -
41S PHE* 3.2 42.4 + + + +
43S TYR* 1.3 103.9 - + + +
45S TRP* 1.3 57.2 + - - +
47S LEU* 3.6 9.8 + - + +
48S MET* 2.9 23.9 + - - +
134m PHE* 5.3 4.8 - - - -
26u LYS* 6.0 4.5 - - - -
94u GLN 5.9 3.4 - - - -
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Residues in contact with TRP 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S ALA* 4.0 8.7 - - + -
41S PHE 3.5 1.4 + - - -
42S GLY 2.9 9.2 + - - +
44S HIS* 1.3 78.3 - - - +
46S SER* 1.3 68.0 + - - +
47S LEU 3.1 1.1 - - - -
48S MET* 3.9 25.2 - - + +
49S GLU* 3.0 61.8 + - - +
135W HIS* 4.4 11.4 + + - -
136W ALA* 4.9 9.2 - - - -
139W GLY* 3.4 38.0 + - - -
140W PHE* 3.6 35.0 - + + -
143W TYR* 4.4 10.8 - + - +
130m GLU* 3.0 35.0 - - - -
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Residues in contact with SER 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S GLY 2.9 8.7 + - - -
43S TYR* 2.6 23.9 + - - -
45S TRP* 1.3 83.0 - - - +
47S LEU* 1.3 58.9 + - - +
49S GLU* 3.7 4.5 + - - +
50S ARG* 2.9 26.4 + - - +
75W LEU* 5.2 5.1 - - - +
105h ARG* 4.6 5.0 - - - +
130m GLU* 5.5 1.3 - - - -
131m GLY 5.0 2.7 - - - -
132m SER* 3.1 28.9 + - - -
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Residues in contact with LEU 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ARG* 5.0 2.9 - - - +
43S TYR* 2.9 50.7 + - + +
44S HIS* 3.7 11.2 - - + +
46S SER* 1.3 77.8 + - - +
48S MET* 1.3 64.2 + - - +
50S ARG* 3.1 11.8 - - + +
51S ASP* 2.9 27.4 + - - +
71W LEU* 5.5 7.0 - - + -
75W LEU* 3.8 26.7 - - + -
22u SER* 3.8 29.4 - - - +
25u LEU* 6.1 2.5 - - + -
26u LYS* 5.1 15.0 - - - +
95u GLN* 5.5 2.5 - - - +
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Residues in contact with MET 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ARG* 4.5 16.4 - - + +
39S ALA* 4.4 6.1 - - + -
44S HIS 2.9 18.2 + - - +
45S TRP* 3.1 23.0 + - + +
47S LEU* 1.3 74.3 - - - +
49S GLU* 1.3 62.4 + - + +
51S ASP* 3.0 13.5 + - - +
52S ARG* 2.9 35.3 + - - +
60S TYR* 3.6 44.1 - - + +
143W TYR* 3.6 48.9 - - + +
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Residues in contact with GLU 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S TRP* 3.0 53.8 + - + +
46S SER* 4.2 3.8 - - - +
48S MET* 1.3 74.6 - - + +
50S ARG* 1.3 60.8 + - - +
52S ARG* 2.8 31.5 + - + +
53S ARG* 3.0 27.2 + - - +
135W HIS* 2.9 31.7 + - + -
136W ALA* 5.9 0.2 - - - -
105h ARG* 2.4 24.3 + - - +
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Residues in contact with ARG 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S SER 2.9 18.2 + - - +
47S LEU* 3.0 30.0 + - + +
49S GLU* 1.3 74.6 - - - +
51S ASP* 1.3 63.7 + - - +
54S ILE* 3.1 32.3 - - + +
74W LEU* 6.2 1.6 - - - +
75W LEU* 4.3 8.3 - - + +
78W GLU* 2.7 40.5 + - - -
103h GLU 3.9 13.1 + - - -
105h ARG* 2.7 55.6 + - + +
17u GLU* 6.0 0.8 - - - +
18u VAL* 2.9 31.1 + - - +
20u ILE 3.7 12.5 + - - -
22u SER* 4.5 5.2 - - - +
25u LEU* 4.3 12.9 - - + +
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Residues in contact with ASP 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ARG* 2.5 42.8 + - - -
47S LEU 2.9 9.7 + - - +
48S MET* 3.3 7.4 - - - +
50S ARG* 1.3 75.6 - - - +
52S ARG* 1.3 66.8 + - - +
54S ILE* 3.3 6.7 + - - +
55S SER* 2.9 24.1 + - - -
60S TYR* 3.9 19.0 - - + +
62S VAL 5.1 2.7 - - - +
21u SER* 3.8 10.1 - - - -
22u SER* 2.5 42.9 + - - -
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Residues in contact with ARG 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S MET* 2.9 24.0 + - - +
49S GLU* 2.8 27.7 + - - +
51S ASP* 1.3 76.7 - - - +
53S ARG* 1.3 65.9 + - + +
55S SER* 2.5 23.5 + - - -
58S ASP* 3.0 56.6 + - - +
59S ARG* 4.3 4.8 - - - +
60S TYR* 3.7 38.4 - - + +
135W HIS* 5.1 16.5 + - - -
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Residues in contact with ARG 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S GLU* 3.0 30.6 + - - +
52S ARG* 1.3 82.7 - - + +
54S ILE* 1.3 60.6 + - - +
55S SER 3.4 0.3 + - - -
56S GLY* 3.4 10.9 + - - -
58S ASP* 4.6 11.0 - - - +
82W ARG* 3.2 46.2 - - - +
101h LYS 3.7 8.3 - - - -
102h GLY* 3.0 33.7 - - - +
104h PRO 3.4 5.3 + - - -
105h ARG* 2.8 64.1 + - - +
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Residues in contact with ILE 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50S ARG* 3.1 56.3 - - + +
51S ASP* 3.5 4.0 - - - +
52S ARG 3.2 0.4 - - - -
53S ARG* 1.3 76.5 - - - +
55S SER* 1.3 64.2 + - - +
56S GLY* 2.9 3.5 + - - -
64S LYS* 3.8 21.8 + - + -
102h GLY 4.2 5.4 - - - +
103h GLU* 4.9 5.4 - - - +
105h ARG* 3.0 9.9 - - - +
18u VAL 4.5 0.4 - - - +
19u LYS* 3.1 38.0 - - + +
20u ILE 3.3 20.2 - - - +
21u SER* 4.4 8.5 - - - +
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Residues in contact with SER 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S ASP 2.9 13.1 + - - -
52S ARG 2.5 21.0 + - - -
54S ILE* 1.3 77.8 - - - +
56S GLY* 1.3 51.9 + - - +
57S VAL* 2.7 22.2 + - - +
58S ASP 3.0 2.5 + - - -
59S ARG 2.9 20.9 + - - -
60S TYR* 3.3 16.0 + - - -
62S VAL* 4.0 20.0 - - - -
64S LYS* 2.5 28.4 + - - +
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Residues in contact with GLY 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S ARG 3.9 0.2 + - - -
53S ARG 3.4 9.6 + - - -
54S ILE 2.9 7.5 + - - -
55S SER* 1.3 77.2 + - - +
57S VAL* 1.3 58.9 + - - -
58S ASP* 2.9 9.8 + - - +
64S LYS* 5.5 0.4 - - - -
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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) + - + + + + + -
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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