Contacts of the helix formed by residues 55 - 68 (chain B) in PDB entry 3GG0
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 GLU 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 3.6 8.7 + - + +
3B THR* 3.4 28.7 + - + +
54B THR* 1.3 74.1 - - - +
56B GLU* 1.3 63.4 + - + +
58B LEU* 4.0 2.1 - - - +
59B GLU* 3.1 52.8 + - + +
79B ARG* 5.6 4.2 + - - +
81B TYR* 3.1 32.5 + - + -
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR* 3.2 5.7 + - - +
55B GLU* 1.3 79.9 - - + +
57B ALA* 1.3 64.3 + - - +
59B GLU* 3.7 13.6 + - - +
60B SER* 3.3 22.7 + - - -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.4 15.7 - - + +
36B ILE* 4.4 24.5 - - + +
53B GLY* 5.4 0.2 - - - -
54B THR* 3.1 27.5 + - - +
56B GLU* 1.3 78.8 - - - +
58B LEU* 1.3 58.7 + - - +
60B SER* 3.4 5.7 + - - -
61B LEU* 3.1 28.6 + - - +
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B THR* 3.4 41.5 - - + +
5B LEU* 3.8 25.1 - - + +
36B ILE* 4.1 22.7 - - + -
51B LEU* 3.5 40.2 - - + +
53B GLY* 3.8 13.9 - - - +
54B THR 3.0 16.2 + - - +
55B GLU* 4.2 3.8 - - - +
57B ALA* 1.3 75.7 - - - +
59B GLU* 1.3 58.7 + - - +
61B LEU* 3.9 3.4 - - + +
62B PHE* 3.0 31.7 + - - +
79B ARG* 5.3 3.8 - - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLU* 3.1 40.8 + - + +
56B GLU* 3.8 16.0 - - - +
58B LEU* 1.3 75.1 - - - +
60B SER* 1.3 65.3 + - - +
62B PHE* 3.4 5.2 + - - +
63B SER* 3.2 25.7 + - - -
79B ARG* 4.2 19.5 - - - +
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU 3.3 16.2 + - - -
57B ALA* 3.7 5.6 - - - -
58B LEU 3.4 0.2 - - - -
59B GLU* 1.3 78.6 - - - +
61B LEU* 1.3 62.4 + - - +
63B SER* 3.4 18.2 - - - -
64B GLU* 3.0 28.3 + - - +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 5.0 3.4 - - - +
31B ASN* 3.9 0.7 - - - +
36B ILE* 3.8 25.6 - - + -
51B LEU* 3.8 30.5 - - + -
57B ALA 3.1 17.0 + - - +
58B LEU* 4.0 6.1 - - + +
60B SER* 1.3 74.8 - - - +
62B PHE* 1.3 59.9 + - - +
64B GLU* 3.1 17.1 + - - +
65B ILE* 2.8 43.2 + - + +
504B FMN 3.4 50.7 - - + +
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Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.6 21.3 - - + +
7B TYR* 3.8 34.5 - + + -
58B LEU 3.0 19.5 + - - +
59B GLU* 3.9 5.6 - - - +
61B LEU* 1.3 73.3 - - - +
63B SER* 1.3 60.3 - - - +
65B ILE* 4.2 12.8 - - + -
66B GLN* 2.8 64.5 + - + +
74B VAL* 3.7 28.5 - - + -
76B GLU* 3.7 31.4 - - + -
79B ARG* 3.6 17.9 - - - +
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU 3.2 13.8 + - - -
60B SER* 3.4 13.1 - - - -
62B PHE* 1.3 77.3 - - - +
64B GLU* 1.3 63.4 + - - +
66B GLN* 3.9 9.9 + - - +
67B SER* 3.2 23.1 + - - -
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 2.4 35.3 + - - -
60B SER* 3.0 30.2 + - - +
61B LEU* 3.1 13.2 + - + +
63B SER* 1.3 81.0 - - - +
65B ILE* 1.3 62.4 + - - +
67B SER* 3.1 17.5 + - - -
68B ASP* 3.1 10.7 + - - +
504B FMN 3.0 26.4 + - - +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B TYR* 3.4 26.0 - - + +
49B GLN* 3.5 21.8 - - - +
51B LEU* 3.9 12.3 - - + -
61B LEU* 2.8 44.4 + - + +
62B PHE* 3.9 13.2 - - + +
64B GLU* 1.3 76.2 - - - +
66B GLN* 1.3 59.4 + - - +
68B ASP* 3.4 5.4 + - - +
71B HIS* 2.6 45.3 + - + -
74B VAL* 5.2 0.7 - - + -
504B FMN 3.5 31.6 - - + +
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 2.8 63.3 + - + +
63B SER* 3.9 8.3 - - - +
65B ILE* 1.3 75.3 - - - +
67B SER* 1.3 59.8 + - - +
68B ASP 3.3 3.2 + - - +
71B HIS* 5.1 0.6 + - - -
74B VAL* 4.0 27.9 - - + +
334B ILE* 5.2 15.1 - - - +
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER 3.2 17.7 + - - -
64B GLU* 3.1 10.0 + - - -
66B GLN* 1.3 77.1 - - - +
68B ASP* 1.3 63.7 + - - +
69B PRO* 3.4 7.8 - - - +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLU 3.1 3.6 + - - +
65B ILE 3.4 15.0 - - - +
66B GLN 3.3 3.6 - - - +
67B SER* 1.3 77.4 - - - +
69B PRO* 1.3 68.2 - - - +
70B ARG* 2.8 61.8 + - - +
71B HIS* 3.0 31.7 - - + +
504B FMN 2.6 41.5 + - + +
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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