Contacts of the strand formed by residues 70 - 78 (chain H) in PDB entry 2N0A
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 VAL 70 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66G VAL* 4.2 7.4 - - + -
69G ALA 3.2 2.4 + - - +
70G VAL* 3.2 28.6 - - + +
71G VAL 3.2 20.6 + - - -
64H THR* 5.4 6.7 - - + -
66H VAL* 3.8 22.9 - - + -
69H ALA* 1.3 78.5 - - - +
71H VAL* 1.3 66.5 + - - +
72H THR* 4.0 20.4 - - + -
70I VAL* 3.2 33.4 - - + +
71I VAL* 5.6 0.4 - - - -
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Residues in contact with VAL 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G VAL* 5.6 0.7 - - - -
71G VAL* 3.3 17.9 - - + +
92G THR* 3.0 35.0 - - - +
70H VAL* 1.3 79.1 - - - +
72H THR* 1.3 69.4 + - - +
75H THR* 4.2 18.6 - - - +
92H THR* 3.6 18.8 - - + +
93H GLY* 3.4 21.1 - - - +
70I VAL 3.2 7.5 + - - -
71I VAL* 3.3 12.0 - - + +
72I THR 3.1 22.5 + - - +
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Residues in contact with THR 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G VAL 3.1 5.4 + - - +
72G THR* 3.1 27.6 - - + +
73G GLY 3.2 20.6 + - - +
61H GLU* 4.9 8.5 + - - +
70H VAL* 4.0 18.8 - - + -
71H VAL* 1.3 82.2 - - - +
73H GLY* 1.3 58.9 + - - +
74H VAL 4.3 0.2 + - - -
61I GLU* 5.3 7.6 - - - +
72I THR* 3.1 28.0 - - + +
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Residues in contact with GLY 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G GLY* 3.3 9.9 - - - -
72H THR* 1.3 75.2 - - - +
74H VAL* 1.3 62.3 + - - +
72I THR 3.2 8.3 + - - +
73I GLY* 3.3 7.6 - - - -
74I VAL* 3.1 24.6 + - - +
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Residues in contact with VAL 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G GLY 3.1 5.4 + - - +
74G VAL* 3.3 28.8 - - + +
75G THR 3.1 23.7 + - - +
51H GLY* 4.7 17.7 - - - -
52H VAL 5.2 2.7 - - - +
53H ALA* 3.8 26.9 - - + +
72H THR 4.3 0.6 - - - -
73H GLY* 1.3 74.4 - - - -
75H THR* 1.3 70.5 + - - +
76H ALA* 5.0 4.5 - - + +
51I GLY* 4.8 8.7 - - - +
53I ALA* 5.3 1.1 - - + -
74I VAL* 3.3 31.0 - - + +
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Residues in contact with THR 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G THR* 3.3 16.5 + - + +
92G THR* 4.1 23.2 - - + +
71H VAL* 4.2 20.3 - - - +
73H GLY 5.5 0.2 - - - -
74H VAL* 1.3 78.4 + - - +
76H ALA* 1.3 63.8 + - - +
77H VAL* 4.5 14.6 - - + -
92H THR* 4.7 9.9 - - + -
74I VAL 3.1 8.0 + - - +
75I THR* 3.3 19.2 + - + +
76I ALA 3.1 23.0 + - - +
77I VAL* 6.2 0.2 - - - -
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Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G THR 3.1 8.2 + - - +
76G ALA* 3.3 7.0 - - + -
77G VAL 3.2 19.6 + - - -
49H VAL* 3.3 24.2 - - + +
50H HIS 5.2 5.8 - - - +
51H GLY* 5.4 2.5 - - - -
74H VAL* 4.4 7.8 - - + +
75H THR* 1.3 75.0 - - - +
77H VAL* 1.3 67.2 + - - +
49I VAL* 3.9 13.2 - - + -
51I GLY* 5.4 4.3 - - - +
76I ALA* 3.3 11.4 - - + +
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Residues in contact with VAL 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G THR* 6.4 0.7 - - + -
77G VAL* 3.4 28.5 - - + +
90G ALA* 3.8 16.8 - - + -
75H THR* 4.5 12.8 - - + -
76H ALA* 1.3 84.8 - - - +
78H ALA* 1.3 57.9 + - - +
79H GLN* 4.3 17.3 - - + +
90H ALA* 4.0 14.6 - - + -
49I VAL* 3.2 11.8 - - - +
76I ALA 3.2 4.4 + - - -
77I VAL* 3.4 29.2 - - + -
78I ALA 3.0 19.3 + - - +
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Residues in contact with ALA 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G VAL 3.0 12.5 + - - +
78G ALA* 4.4 1.6 - - - -
79G GLN* 2.4 38.5 + - - +
47H GLY 3.9 3.4 - - - -
48H VAL* 3.5 44.4 - - - +
77H VAL* 1.3 71.6 - - - +
79H GLN* 1.3 59.5 + - - +
47I GLY 3.7 9.9 - - - +
49I VAL* 3.9 5.6 - - + +
78I ALA* 4.1 4.3 - - - -
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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