Contacts of the helix formed by residues 69 - 79 (chain F) in PDB entry 4GOM
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 ARG 69 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ILE* 2.9 30.4 + - - +
68F MET* 1.3 88.0 - - + +
70F THR* 1.3 68.2 + - - +
71F ASP 3.2 2.5 + - - -
72F GLU* 2.7 52.2 + - + +
73F TYR* 3.0 17.2 + - - +
103F ASP* 5.7 0.4 + - - -
104F PRO* 6.2 0.4 - - - +
105F PHE* 3.4 45.0 - - + +
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Residues in contact with THR 70 (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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66F VAL* 2.9 24.4 + - + +
67F LYS 3.4 9.7 + - - -
68F MET 3.7 1.4 - - - -
69F ARG* 1.3 77.6 - - - +
71F ASP* 1.3 66.6 + - - +
73F TYR* 3.0 11.6 + - - +
74F VAL* 3.1 21.9 + - + +
148F LEU 5.0 1.3 - - - +
149F TYR* 3.7 28.0 - - + -
152F ALA* 3.5 27.3 - - + +
156F GLN* 4.7 2.4 + - - -
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Residues in contact with ASP 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F ARG 3.4 0.6 - - - -
70F THR* 1.3 81.7 - - - +
72F GLU* 1.3 62.4 + - - +
74F VAL* 3.6 1.9 + - - +
75F GLN* 3.2 25.5 + - - +
149F TYR* 2.9 35.3 + - - -
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Residues in contact with GLU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F ARG* 2.7 56.9 + - + +
70F THR 3.4 0.2 - - - -
71F ASP* 1.3 79.2 - - - +
73F TYR* 1.3 60.4 + - - +
75F GLN* 4.2 3.8 - - - +
76F ALA* 3.2 24.1 + - + +
105F PHE* 3.5 15.5 - - + -
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Residues in contact with TYR 73 (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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62F LEU* 3.5 11.5 - - + +
65F ILE* 3.9 24.0 - - + +
66F VAL* 4.2 12.3 - - + -
69F ARG 3.0 15.1 + - - +
70F THR* 3.0 9.2 + - - +
72F GLU* 1.3 72.7 - - - +
74F VAL* 1.3 73.9 + - + +
75F GLN 3.1 1.7 + - - -
76F ALA* 3.2 3.1 + - - +
77F ALA* 2.9 34.1 + - + +
105F PHE* 3.8 11.9 - + + -
108F ALA* 2.9 41.5 + - + -
109F VAL* 3.8 18.3 - - + -
112F LEU* 3.3 25.3 - - + +
148F LEU* 3.7 31.0 - - + -
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Residues in contact with VAL 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F VAL* 6.5 0.7 - - + -
70F THR* 3.1 20.0 + - + +
71F ASP 4.0 2.2 - - - +
73F TYR* 1.3 82.8 - - + +
75F GLN* 1.4 62.6 + - - +
77F ALA* 4.8 2.5 - - - -
78F ARG* 3.1 45.1 + - - +
143F PHE* 3.7 19.3 - - + -
145F GLU* 4.4 3.8 - - + -
148F LEU* 4.4 22.2 - - + -
149F TYR* 3.9 39.7 - - + +
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Residues in contact with GLN 75 (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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71F ASP 3.2 15.8 + - - +
72F GLU* 4.2 4.5 - - - +
73F TYR 3.1 0.8 - - - -
74F VAL* 1.4 80.4 - - - +
76F ALA* 1.3 64.0 + - - +
78F ARG* 3.3 28.9 + - - +
79F GLU* 3.7 20.2 + - - +
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Residues in contact with ALA 76 (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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72F GLU 3.2 16.8 + - - +
73F TYR 3.2 4.0 + - - +
75F GLN* 1.3 80.3 - - - +
77F ALA* 1.3 60.4 + - - +
79F GLU* 3.4 26.0 - - - +
80F LEU* 4.3 4.9 + - - +
105F PHE* 3.9 22.2 - - + -
109F VAL* 4.0 15.8 - - + +
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Residues in contact with ALA 77 (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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73F TYR* 2.9 38.5 + - + +
74F VAL 4.1 1.6 - - - +
76F ALA* 1.3 73.8 - - - +
78F ARG* 1.3 64.7 + - - +
79F GLU 3.1 2.5 - - - -
80F LEU* 3.2 11.9 + - - +
81F PHE* 3.3 19.6 - - + -
109F VAL* 3.9 19.3 - - + +
112F LEU* 4.1 17.0 - - + -
143F PHE* 3.8 6.3 - - + -
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Residues in contact with ARG 78 (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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74F VAL* 3.1 31.0 + - - +
75F GLN* 3.7 21.8 + - - +
76F ALA 3.3 0.8 - - - -
77F ALA* 1.3 76.6 - - - +
79F GLU* 1.3 55.5 + - + +
81F PHE* 2.8 30.1 + - + +
82F VAL* 4.3 3.8 + - - +
143F PHE* 3.7 25.4 - - + -
145F GLU* 2.8 39.8 + - - -
149F TYR* 4.9 4.4 + - - -
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Residues in contact with GLU 79 (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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75F GLN* 3.8 16.9 - - - +
76F ALA* 3.4 17.3 - - - +
77F ALA 3.1 0.2 - - - -
78F ARG* 1.3 78.9 - - + +
80F LEU* 1.3 66.5 - - + +
81F PHE 3.4 0.4 - - - -
82F VAL* 3.8 23.1 - - - +
85F THR* 5.0 0.9 - - - +
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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