Contacts of the helix formed by residues 47 - 61 (chain F) in PDB entry 3SWD
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 LEU 47 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F LYS* 4.1 20.0 - - + -
45F PRO* 3.3 26.3 + - + +
46F LYS* 1.3 75.7 - - - +
48F LYS* 1.3 68.0 + - - +
49F ASP 3.2 1.8 - - - +
50F VAL* 3.0 41.6 + - + +
51F ASP* 3.3 16.2 + - - -
66F ARG* 4.7 1.0 - - - +
231F ASP* 5.9 0.2 - - - +
396F ASP 3.4 14.1 - - - +
397F ARG 3.7 11.7 - - - +
398F GLY 3.6 29.8 - - - +
399F TYR 3.7 7.0 - - - +
400F GLU 3.9 10.1 - - - +
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Residues in contact with LYS 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LEU* 1.3 70.0 - - - +
49F ASP* 1.3 62.9 + - - +
51F ASP* 3.1 25.2 + - - +
52F THR* 3.1 30.8 + - - +
393F TYR 5.4 0.4 - - - +
396F ASP* 3.1 25.8 + - + +
397F ARG* 3.9 18.8 - - + -
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Residues in contact with ASP 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LYS* 3.1 27.1 + - - -
26F LEU* 4.0 22.2 - - + +
47F LEU* 3.1 3.8 + - + -
48F LYS* 1.3 76.2 - - - +
50F VAL* 1.3 59.2 + - - +
52F THR* 3.5 3.0 + - - -
53F SER* 3.1 26.2 + - - -
90F MET* 3.6 22.7 - - - +
370F LEU* 3.4 8.2 - - - +
397F ARG* 2.9 51.1 + - - +
501F EPZ 4.3 2.3 - - - +
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ALA* 4.5 7.9 - - + -
26F LEU* 4.1 14.1 - - + -
29F LEU* 4.1 13.7 - - + -
44F VAL* 3.8 18.2 - - + -
45F PRO* 3.6 21.1 - - + +
47F LEU* 3.0 21.7 + - + +
49F ASP* 1.3 73.1 - - - +
51F ASP* 1.3 66.8 - - - +
53F SER* 3.1 8.6 + - - -
54F MET* 2.9 37.6 + - + +
66F ARG* 4.0 20.2 - - - +
70F VAL* 5.2 1.3 - - + -
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Residues in contact with ASP 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LEU 3.3 14.2 + - - +
48F LYS* 3.1 32.8 + - + +
50F VAL* 1.3 77.8 - - - +
52F THR* 1.3 56.9 + - - +
54F MET* 3.2 27.0 + - + +
55F LYS* 2.9 28.5 + - - +
66F ARG* 4.9 5.0 + - - -
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Residues in contact with THR 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LYS* 3.1 24.4 + - - +
49F ASP* 3.8 9.5 + - - -
50F VAL 3.3 0.2 - - - -
51F ASP* 1.3 76.5 - - - +
53F SER* 1.3 61.8 + - - +
55F LYS* 3.4 7.9 + - + -
56F LEU* 3.1 22.0 + - - +
86F LEU* 3.8 20.2 - - + +
89F THR* 3.9 22.2 + - - +
90F MET* 4.0 27.6 - - + +
93F SER* 5.0 0.4 - - - +
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Residues in contact with SER 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 3.6 19.9 - - - +
29F LEU* 3.9 23.1 - - - -
30F PHE* 3.7 21.4 - - - -
49F ASP 3.1 14.4 + - - -
50F VAL 3.1 8.8 + - - -
52F THR* 1.3 74.7 - - - +
54F MET* 1.3 59.8 + - - +
56F LEU* 3.2 3.9 + - - +
57F LEU* 2.9 34.2 + - - +
90F MET* 3.6 9.7 - - - +
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Residues in contact with MET 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LEU* 4.6 9.4 - - + -
50F VAL* 2.9 20.5 + - + +
51F ASP* 3.2 36.3 - - + +
53F SER* 1.3 73.2 - - - +
55F LYS* 1.3 59.2 + - - +
57F LEU* 3.1 9.8 + - + +
58F SER* 2.8 32.9 + - - -
64F VAL* 3.7 26.3 - - + +
65F GLU* 5.0 1.8 - - - -
66F ARG* 3.8 24.5 - - + -
70F VAL* 3.7 27.4 - - + -
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Residues in contact with LYS 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ASP 2.9 16.8 + - - +
52F THR* 3.8 8.5 - - + +
53F SER 3.3 0.2 - - - -
54F MET* 1.3 75.9 - - - +
56F LEU* 1.3 61.9 + - - +
58F SER* 3.4 6.3 + - - -
59F GLN* 3.0 38.5 + - + +
86F LEU* 4.0 24.5 - - + +
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Residues in contact with LEU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F PHE* 3.5 28.3 - - + -
52F THR 3.1 10.3 + - - +
53F SER* 3.7 6.7 - - - +
55F LYS* 1.3 72.7 - - - +
57F LEU* 1.3 67.0 + - - +
59F GLN* 3.0 17.8 + - + +
60F LEU* 3.1 28.3 + - + +
81F CYS 4.5 0.2 - - - +
82F ALA* 3.9 32.3 - - + -
83F PRO* 4.3 7.4 - - + -
86F LEU* 3.3 24.0 - - + +
93F SER* 3.7 29.8 - - - +
96F ALA* 4.3 4.3 - - + -
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Residues in contact with LEU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LEU* 3.6 39.0 - - + +
30F PHE* 4.3 18.6 - - + -
32F ALA* 5.8 0.2 - - + -
33F LEU* 4.0 26.5 - - + -
53F SER* 2.9 19.5 + - - +
54F MET* 3.4 9.9 - - - +
56F LEU* 1.3 74.5 - - - +
58F SER* 1.3 64.2 + - - +
60F LEU* 3.0 19.0 + - + +
61F GLY 3.4 0.2 + - - -
62F ALA* 3.2 26.8 + - + +
64F VAL* 3.8 15.3 - - + -
72F ILE* 3.9 26.7 - - + -
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Residues in contact with SER 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F MET 2.8 20.6 + - - -
55F LYS* 3.7 7.0 - - - -
57F LEU* 1.3 73.3 - - - +
59F GLN* 1.3 57.4 + - - +
61F GLY* 2.8 22.3 + - - -
62F ALA 3.6 15.8 + - - +
64F VAL* 4.3 9.3 + - - +
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Residues in contact with GLN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LYS* 3.0 32.7 + - + +
56F LEU* 3.0 11.9 + - + +
58F SER* 1.3 74.9 - - - +
60F LEU* 1.3 53.5 + - + +
61F GLY* 3.2 1.2 + - - -
79F VAL* 2.6 27.7 - - + +
81F CYS 5.8 1.8 - - - +
83F PRO* 3.7 25.5 - - - +
86F LEU* 3.3 25.6 - - - +
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 3.6 36.8 - - + -
56F LEU* 3.1 32.2 + - + +
57F LEU* 3.0 13.8 + - + +
59F GLN* 1.3 75.6 - - - +
61F GLY* 1.3 57.7 + - - +
62F ALA 4.9 0.2 - - - +
77F VAL* 3.4 11.6 - - + +
78F ASN 3.0 17.5 + - - -
79F VAL* 3.0 42.0 + - + +
80F PHE 4.3 2.5 - - - -
81F CYS 3.7 34.8 - - - +
82F ALA* 4.7 0.7 - - + +
96F ALA* 4.6 4.3 - - + -
100F LEU* 4.2 13.0 - - + -
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Residues in contact with GLY 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F SER 2.8 10.8 + - - -
59F GLN 3.0 2.5 - - - -
60F LEU* 1.3 80.7 - - - +
62F ALA* 1.3 63.4 + - - +
63F LYS* 4.0 6.1 + - - +
73F ASP 4.6 0.3 - - - +
76F ASP* 3.3 26.3 + - - +
77F VAL* 4.1 3.6 - - - -
78F ASN* 3.7 15.3 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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