Contacts of the helix formed by residues 49 - 64 (chain F) in PDB entry 2GZJ
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 49 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F ARG 3.6 4.5 - - - -
6F ASN* 3.9 23.6 - - - +
47F PHE* 3.3 2.3 - - - +
48F LYS* 1.3 79.7 - - - +
50F PHE* 1.3 64.6 + - - +
51F ASP* 3.4 9.2 + - - +
52F ASP* 3.1 29.2 + - - +
53F PHE 3.2 15.6 + - - -
114F TYR* 3.0 18.2 + - - -
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Residues in contact with PHE 50 (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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5F ARG* 2.8 51.9 + - + +
49F SER* 1.3 71.4 - - - +
51F ASP* 1.3 62.6 + - - +
53F PHE* 3.1 23.7 + + + +
54F ARG* 2.8 32.7 + - + +
101F LEU* 4.0 44.4 - - + -
103F HIS* 3.5 25.6 - + - -
113F VAL* 3.4 34.8 - - + -
114F TYR* 3.4 7.0 + + - -
119F ILE* 3.9 10.1 - - + -
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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
----------------------------------------------------------
5F ARG* 5.3 6.1 + - - -
6F ASN* 4.9 9.5 + - - +
49F SER* 3.3 8.8 + - - +
50F PHE* 1.3 81.8 - - - +
52F ASP* 1.3 63.6 + - - +
54F ARG* 3.3 18.5 + - - +
55F LYS* 3.1 22.2 + - - +
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Residues in contact with ASP 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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47F PHE* 4.0 10.4 - - + -
48F LYS* 3.4 32.5 + - - +
49F SER* 3.1 26.0 + - - +
51F ASP* 1.3 78.2 - - - +
53F PHE* 1.3 62.6 + - - +
55F LYS* 3.4 13.7 + - - +
56F ALA* 3.2 20.4 + - - +
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Residues in contact with PHE 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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11F ALA* 4.1 11.0 - - + -
34F ILE* 5.2 2.2 - - + -
42F LEU* 3.9 17.5 - - + -
47F PHE* 3.8 32.0 - + + -
49F SER 3.2 4.2 + - - +
50F PHE* 3.1 27.9 + + - +
52F ASP* 1.3 75.5 - - - +
54F ARG* 1.3 68.5 + - - +
56F ALA* 3.1 4.9 + - - +
57F VAL* 3.0 43.6 + - + +
101F LEU* 4.3 6.5 - - + -
114F TYR* 3.9 26.7 - + + -
116F MET* 3.6 34.1 - - + -
119F ILE* 3.6 23.1 - - + -
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Residues in contact with ARG 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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30E GLU* 2.6 46.8 + - - +
50F PHE* 2.8 21.3 + - + +
51F ASP* 3.4 20.6 - - - +
53F PHE* 1.3 76.2 - - - +
55F LYS* 1.3 62.9 + - - +
57F VAL* 3.2 11.3 + - - +
58F TRP* 3.2 31.6 + - + +
82F GLY 4.6 6.5 + - - -
84F SER* 3.6 21.9 - - - +
98F VAL* 3.9 7.7 - - - +
99F TYR 4.1 5.3 + - - -
100F GLU* 5.6 2.2 - - - +
101F LEU* 4.0 32.2 - - + +
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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 3.1 10.6 + - - +
52F ASP* 3.5 15.5 - - - +
53F PHE 3.3 0.2 - - - -
54F ARG* 1.3 79.2 - - - +
56F ALA* 1.3 58.3 + - - +
58F TRP 3.3 1.4 + - - -
59F GLU* 3.0 54.3 + - - +
81F LYS 3.5 17.6 + - - -
82F GLY* 3.6 23.7 - - - +
83F TYR* 5.6 2.6 - - - -
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Residues in contact with ALA 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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42F LEU* 4.0 16.4 - - + -
45F LYS* 6.1 1.1 - - + +
47F PHE* 3.5 28.9 - - + -
52F ASP 3.2 4.9 + - - +
53F PHE 3.1 9.7 + - - +
55F LYS* 1.3 77.7 - - - +
57F VAL* 1.3 65.1 + - - +
59F GLU* 3.4 13.8 + - - +
60F GLU* 3.0 28.9 + - - +
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Residues in contact with VAL 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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22F TRP* 5.5 4.3 - - + -
34F ILE* 4.6 19.1 - - + -
35F PRO* 6.2 0.7 - - + -
38F ILE* 4.4 11.2 - - + +
42F LEU* 3.8 14.8 - - + +
53F PHE* 3.0 48.8 + - + +
54F ARG* 3.2 8.0 + - - +
56F ALA* 1.3 75.7 - - - +
58F TRP* 1.3 83.6 + - + +
60F GLU* 3.2 5.5 + - - +
61F VAL* 3.0 27.1 + - + +
101F LEU* 4.4 12.6 - - + -
121F VAL* 5.9 0.4 - - + -
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Residues in contact with TRP 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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22F TRP* 4.0 14.6 - + - -
23F LEU* 4.3 6.3 - - + -
54F ARG* 3.2 38.6 + - + +
55F LYS 3.3 0.4 + - - +
56F ALA 3.3 0.2 - - - -
57F VAL* 1.3 82.8 - - + +
59F GLU* 1.3 62.4 + - - +
61F VAL* 3.2 27.3 + - + +
62F SER 3.0 18.5 + - - -
79F VAL* 3.4 17.3 - - + +
82F GLY* 4.0 14.6 - - - +
83F TYR 3.5 19.5 - - - +
84F SER* 3.5 36.7 - - - -
85F PRO* 3.5 30.5 - - + -
99F TYR* 4.0 13.4 + - + -
101F LEU* 4.3 22.0 - - + +
121F VAL* 4.0 20.2 - - + -
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Residues in contact with GLU 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 54.4 + - - +
56F ALA* 3.7 13.4 - - - +
58F TRP* 1.3 76.4 - - - +
60F GLU* 1.3 62.4 + - + +
62F SER* 3.3 6.5 + - - -
63F LYS* 3.2 33.8 + - - +
79F VAL 3.8 6.3 - - - +
80F SER 4.6 6.8 - - - +
81F LYS 4.5 1.6 - - - +
82F GLY* 3.7 17.3 + - - +
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Residues in contact with GLU 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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38F ILE* 3.3 24.5 - - + +
41F LYS* 3.6 31.3 - - + +
42F LEU* 3.7 26.4 - - + +
45F LYS* 4.3 10.7 + - - -
56F ALA* 3.0 18.5 + - - +
57F VAL 3.2 5.1 + - - +
59F GLU* 1.3 73.2 - - - +
61F VAL* 1.3 66.6 + - - +
63F LYS* 3.1 37.2 + - - +
64F ASP* 3.1 24.9 + - - +
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Residues in contact with VAL 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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22F TRP* 3.8 27.8 - - + -
23F LEU* 6.0 1.1 - - + -
38F ILE* 4.2 12.8 - - + -
57F VAL* 3.0 22.5 + - + +
58F TRP* 3.2 33.0 + - + +
60F GLU* 1.3 76.4 - - - +
62F SER* 1.3 62.5 + - - +
63F LYS 3.2 0.9 + - - -
64F ASP 3.2 19.8 + - - +
67F LEU* 4.3 20.2 - - + +
68F SER* 3.4 6.1 + - - -
71F LEU* 4.2 25.1 - - + -
79F VAL* 4.5 2.2 - - + -
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Residues in contact with SER 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 TRP 3.0 5.4 + - - -
59F GLU* 3.3 12.3 - - - -
61F VAL* 1.3 75.4 - - - +
63F LYS* 1.3 60.7 + - - +
64F ASP 3.7 0.3 + - - -
68F SER* 4.0 13.6 + - - -
76F LYS 4.5 1.2 + - - -
79F VAL* 3.6 36.3 - - - +
80F SER* 3.3 22.1 + - - -
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Residues in contact with LYS 63 (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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45F LYS* 5.5 3.2 - - - +
59F GLU* 3.3 18.8 - - + +
60F GLU* 3.1 45.1 + - - +
61F VAL 3.1 0.4 - - - -
62F SER* 1.3 79.2 - - - +
64F ASP* 1.3 57.9 + - - +
65F PRO* 3.4 11.2 - - - +
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Residues in contact with ASP 64 (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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37F ARG* 2.8 45.8 + - - +
38F ILE* 4.9 2.7 - - + +
41F LYS* 4.7 7.6 + - - +
60F GLU 3.1 14.3 + - - +
61F VAL 3.2 3.5 + - - +
63F LYS* 1.3 75.6 - - - +
65F PRO* 1.3 62.4 - - - +
66F GLU* 2.9 17.8 + - - +
67F LEU* 3.0 26.4 + - + +
68F SER* 2.9 28.6 + - - -
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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