Contacts of the helix formed by residues 47 - 62 (chain F) in PDB entry 5GAG
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 LYS 47 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43F ALA* 3.4 20.2 - - + +
44F ILE* 3.9 18.8 - - - +
45F ALA 5.7 0.7 - - - +
46F ASP* 1.3 73.1 + - - +
48F LYS* 1.3 62.8 + - + +
50F LEU* 2.9 24.2 + - + +
51F ASP* 3.1 17.5 - - - +
83F TYR* 5.3 7.9 - - - -
84F PRO* 4.1 31.0 - - + +
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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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46F ASP* 3.3 30.2 + - - +
47F LYS* 1.3 78.5 - - + +
49F LEU* 1.3 57.8 + - - +
50F LEU 3.0 0.2 - - - -
51F ASP* 2.9 17.1 + - - +
52F ASN* 2.8 50.1 + - - +
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Residues in contact with LEU 49 (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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40F VAL* 4.4 7.0 - - + +
42F GLU* 3.4 36.3 - - + +
43F ALA* 4.5 4.9 - - - -
46F ASP* 3.4 30.9 + - + +
47F LYS 3.1 0.6 - - - -
48F LYS* 1.3 77.1 - - - +
50F LEU* 1.3 58.4 + - - +
52F ASN* 3.8 4.0 - - - +
53F ALA* 3.4 19.9 + - - +
147F ASP* 3.4 18.6 - - - +
148F ARG* 3.8 20.0 - - + +
150F ARG* 3.4 29.9 + - - +
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F VAL* 3.5 23.3 - - + -
43F ALA* 3.9 14.5 - - + +
47F LYS* 2.9 13.3 + - + +
49F LEU* 1.3 78.8 - - - +
51F ASP* 1.3 57.5 + - - +
53F ALA* 3.0 5.5 + - + +
54F ALA* 2.6 32.5 + - + +
67F ILE* 3.9 23.8 - - + -
84F PRO* 3.6 32.3 - - + +
85F ILE 4.8 0.7 - - - -
86F GLY* 3.7 23.3 - - - +
87F CYS* 3.7 20.0 - - + -
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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
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47F LYS* 3.1 17.4 - - - +
48F LYS* 2.9 26.0 + - - +
50F LEU* 1.3 76.3 - - - +
52F ASN* 1.3 65.6 + - - +
54F ALA* 2.9 23.6 + - - +
55F ALA* 3.0 14.2 + - - +
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Residues in contact with ASN 52 (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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46F ASP* 5.4 0.6 + - - -
48F LYS* 2.8 40.8 + - - +
49F LEU* 3.8 7.5 - - - +
51F ASP* 1.3 73.0 - - - +
53F ALA* 1.3 59.8 + - - +
55F ALA* 3.8 7.5 - - - +
56F ASP* 3.3 23.0 + - - +
147F ASP* 4.0 19.3 + - - +
150F ARG* 3.6 16.6 + - - +
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Residues in contact with ALA 53 (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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38F MET* 3.6 16.4 - - + +
40F VAL* 4.5 11.7 - - + -
49F LEU 3.4 14.9 + - - +
50F LEU* 3.0 15.5 + - + +
52F ASN* 1.3 76.1 - - - +
54F ALA* 1.3 66.0 - - - +
56F ASP* 3.0 22.1 + - - +
57F LEU* 3.1 10.9 + - - +
87F CYS* 4.6 1.8 - - - -
150F ARG* 3.5 22.2 - - - +
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Residues in contact with ALA 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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50F LEU 2.6 16.7 + - - +
51F ASP* 3.2 14.6 - - - +
53F ALA* 1.3 72.4 - - - +
55F ALA* 1.3 53.0 + - - +
57F LEU 3.0 3.5 + - - -
58F ALA* 2.7 33.2 + - - +
65F PRO* 3.4 28.4 - - + +
67F ILE* 5.4 8.5 - - + -
87F CYS* 4.3 9.8 - - - -
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Residues in contact with ALA 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 3.0 10.3 + - - +
52F ASN* 3.8 12.6 - - - +
54F ALA* 1.3 75.2 - - - +
56F ASP* 1.3 64.3 + - - +
58F ALA* 3.0 10.5 + - - +
59F ALA* 2.9 23.9 + - - +
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Residues in contact with ASP 56 (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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38F MET* 3.7 13.5 - - + -
52F ASN 3.3 13.3 + - - +
53F ALA* 3.0 8.9 + - - +
55F ALA* 1.3 77.9 - - - +
57F LEU* 1.3 64.5 + - - +
59F ALA* 3.0 15.6 + - - +
60F ILE* 3.0 20.0 + - + +
135F GLN* 4.4 15.5 + - + +
141F ILE* 3.7 20.2 - - + +
146F VAL* 5.9 2.8 - - - +
147F ASP* 4.9 0.3 - - - +
150F ARG* 3.0 35.9 + - - +
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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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36F LEU* 3.8 46.9 - - + +
38F MET* 3.7 25.3 - - + +
53F ALA 3.1 6.1 + - - +
54F ALA* 3.0 9.0 + - - +
56F ASP* 1.3 77.8 - - - +
58F ALA* 1.3 57.8 + - - +
60F ILE* 3.0 8.0 + - + +
61F SER* 2.8 39.5 + - - +
65F PRO* 3.7 9.4 - - + -
87F CYS* 3.8 33.2 - - - +
88F LYS 4.1 1.3 - - - -
89F VAL* 4.1 18.2 - - + +
152F LEU* 5.0 3.8 - - + -
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Residues in contact with ALA 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 ALA 2.7 16.8 + - - +
55F ALA* 3.0 18.4 + - - +
57F LEU* 1.3 73.2 - - - +
59F ALA* 1.3 54.6 + - - +
62F GLY* 3.1 26.9 + - - -
63F GLN 3.8 17.2 + - - +
64F LYS* 5.2 0.9 - - - -
65F PRO* 3.8 14.1 - - + +
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Residues in contact with ALA 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 ALA 2.9 11.0 + - - +
56F ASP* 3.5 7.9 - - - +
58F ALA* 1.3 75.5 - - - +
60F ILE* 1.3 64.2 + - - +
62F GLY* 4.2 4.0 + - - -
140F GLU* 3.2 36.6 - - + +
141F ILE* 4.3 10.1 - - + -
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Residues in contact with ILE 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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36F LEU* 4.1 8.7 - - + -
38F MET* 3.8 8.1 - - + -
56F ASP* 3.3 22.7 - - + +
57F LEU* 3.0 7.7 + - + +
59F ALA* 1.3 79.4 - - - +
61F SER* 1.3 61.4 + - - +
99F PHE* 3.7 13.7 - - + -
102F ARG* 2.9 29.3 + - - -
135F GLN* 4.6 3.6 - - + -
138F PHE* 3.6 43.3 - - + -
140F GLU* 4.4 6.2 - - - +
141F ILE* 3.6 21.8 - - + -
152F LEU* 3.6 28.0 - - + -
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Residues in contact with SER 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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36F LEU* 4.0 18.2 - - - -
57F LEU* 2.8 25.1 + - - -
60F ILE* 1.3 74.8 - - - +
62F GLY* 1.3 60.5 + - - +
63F GLN 3.4 18.5 + - - -
89F VAL* 3.6 30.2 - - - +
91F LEU* 3.9 21.3 - - - +
95F ARG* 4.7 6.2 + - - +
99F PHE* 4.7 1.8 - - - -
102F ARG* 3.6 16.0 + - - -
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Residues in contact with GLY 62 (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 ALA 3.1 14.6 + - - -
59F ALA 4.2 3.5 + - - -
60F ILE 3.6 0.6 - - - -
61F SER* 1.3 80.2 + - - +
63F GLN* 1.3 64.9 + - - +
95F ARG* 3.9 24.2 + - - -
102F ARG* 5.5 0.2 - - - -
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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