Contacts of the helix formed by residues 64 - 74 (chain L) in PDB entry 6GE3
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 ASP 64 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62L GLU* 3.5 25.1 - - - +
63L THR* 1.3 80.8 + - - +
65L LEU* 1.3 59.3 + - - +
66L GLU* 3.5 10.0 + - - +
67L ALA* 3.2 23.1 + - - +
68L LEU* 2.9 27.8 + - - +
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Residues in contact with LEU 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A TYR* 3.7 45.3 - - + +
372A ASN* 4.8 16.6 - - + +
373A PHE* 3.9 24.0 - - + +
376A LYS* 4.0 26.0 - - + -
64L ASP* 1.3 75.6 - - - +
66L GLU* 1.3 64.1 + - + +
68L LEU* 3.3 18.4 + - + +
69L PHE* 3.3 26.3 + - + -
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Residues in contact with GLU 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LYS* 2.8 36.6 + - - -
64L ASP* 3.5 7.8 + - - +
65L LEU* 1.3 79.1 - - + +
67L ALA* 1.3 52.3 + - - +
68L LEU 3.3 0.2 + - - -
69L PHE* 3.3 5.2 + - - +
70L ASN* 2.7 38.9 + - + +
73L MET* 5.7 3.8 - - - +
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Residues in contact with ALA 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L GLU* 4.2 15.5 - - + +
64L ASP* 3.2 29.4 + - - +
66L GLU* 1.3 77.3 - - - +
68L LEU* 1.3 57.9 + - - +
70L ASN* 3.7 9.7 + - - +
71L ALA* 2.9 32.6 + - - +
79L ASN* 5.1 3.8 + - + +
80L VAL* 3.6 18.1 - - + +
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Residues in contact with LEU 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A SER* 4.0 18.4 - - - +
337A PHE* 3.5 31.2 - - + -
369A TYR* 4.5 3.8 - - - +
373A PHE* 3.6 31.2 - - + -
389A VAL* 4.0 27.6 - - + +
392A ASN* 4.6 5.6 - - + +
393A PHE* 5.6 1.3 - - + -
63L THR 5.6 1.3 - - - +
64L ASP 2.9 13.7 + - - +
65L LEU* 3.4 16.8 - - + +
66L GLU 3.2 0.2 - - - -
67L ALA* 1.3 78.4 - - - +
69L PHE* 1.3 67.0 + - + +
71L ALA* 3.7 11.4 + - - +
72L VAL* 3.9 13.3 - - - +
80L VAL* 4.2 8.2 - - - +
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Residues in contact with PHE 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A PHE* 3.7 33.9 - + - -
376A LYS* 3.5 37.2 - - + -
377A LEU* 3.5 33.2 - - + -
380A LEU* 3.8 28.3 - - + -
389A VAL* 3.8 20.6 - - + -
65L LEU* 3.3 23.1 + - + +
66L GLU* 4.1 6.7 - - - +
68L LEU* 1.3 81.1 - - + +
70L ASN* 1.3 60.7 + - - +
71L ALA 3.3 0.2 - - - -
72L VAL* 3.2 3.8 + - - +
73L MET* 2.8 48.0 + - + +
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Residues in contact with ASN 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L GLU* 2.7 24.6 + - + +
67L ALA* 3.7 10.4 + - - +
69L PHE* 1.3 72.8 - - - +
71L ALA* 1.3 57.5 + - - +
73L MET* 4.2 4.6 - - - +
74L ASN* 2.7 63.0 + - - +
77L THR* 3.3 40.6 + - - -
78L ALA* 4.3 1.6 - - - +
79L ASN 5.2 1.0 - - - +
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Residues in contact with ALA 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L ALA 2.9 18.3 + - - +
68L LEU 3.7 7.2 - - - +
69L PHE 3.3 0.2 - - - -
70L ASN* 1.3 74.9 - - - +
72L VAL* 1.3 61.5 + - + +
75L PRO* 3.4 24.4 - - - +
78L ALA* 3.7 27.3 - - + +
80L VAL* 3.7 29.2 - - + -
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Residues in contact with VAL 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A LEU* 5.2 3.4 - - + -
384A TYR* 5.8 2.2 - - + -
385A MET* 3.6 53.0 - - + +
388A SER* 4.0 20.6 - - - +
389A VAL* 3.7 27.1 - - + +
68L LEU 3.9 8.1 - - - +
69L PHE 3.2 6.3 + - - +
70L ASN 3.2 0.4 - - - -
71L ALA* 1.3 81.3 - - + +
73L MET* 1.3 64.3 + - - +
74L ASN 3.7 0.2 + - - -
75L PRO* 3.8 9.7 - - - +
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Residues in contact with MET 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A HIS 5.7 2.2 - - - +
380A LEU* 3.5 28.7 - - + -
381A PRO* 5.0 6.7 - - + -
385A MET* 4.7 16.3 - - + +
66L GLU* 5.7 4.3 - - - +
69L PHE* 2.8 45.8 + - + +
70L ASN* 4.2 3.6 - - - +
72L VAL* 1.3 75.3 - - - +
74L ASN* 1.3 76.5 + - - +
75L PRO* 3.4 7.2 - - - +
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Residues in contact with ASN 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ASN* 2.7 38.9 + - - +
73L MET* 1.3 92.2 + - - +
75L PRO* 1.3 64.8 - - - +
76L LYS* 3.1 5.6 + - + -
77L THR* 3.1 27.0 + - + +
78L ALA 3.6 2.8 + - - -
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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