Contacts of the helix formed by residues 49 - 61 (chain H) in PDB entry 2H61
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 49 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33H LYS* 5.8 1.6 - - - -
47H ILE* 3.6 7.2 - - - +
48H LYS* 1.3 92.7 - - + +
50H GLN* 1.3 66.0 + - - +
51H GLU* 4.2 9.0 - - + +
52H VAL* 3.3 29.8 + - + +
53H VAL* 3.4 9.8 + - - +
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Residues in contact with GLN 50 (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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29H LYS* 3.8 19.6 - - - +
33H LYS* 5.5 4.0 - - - +
48H LYS 4.3 0.6 + - - -
49H GLU* 1.3 71.4 + - - +
51H GLU* 1.3 55.4 + - - +
53H VAL* 3.2 18.2 + - - +
54H ASP* 2.8 65.9 + - - +
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Residues in contact with GLU 51 (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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49H GLU* 3.3 8.8 - - + +
50H GLN* 1.3 75.6 - - - +
52H VAL* 1.3 61.0 + - + +
54H ASP* 3.4 9.3 + - - +
55H LYS* 2.9 30.2 + - - +
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Residues in contact with VAL 52 (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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46H GLU 5.9 0.4 - - - +
47H ILE* 3.8 28.7 - - + -
48H LYS 6.0 0.4 - - - +
49H GLU* 3.3 25.0 + - + +
50H GLN 3.1 0.8 - - - -
51H GLU* 1.3 80.6 - - + +
53H VAL* 1.3 60.3 + - - +
55H LYS* 3.2 7.4 + - - +
56H VAL* 3.0 33.4 + - + +
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Residues in contact with VAL 53 (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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29H LYS* 3.8 31.6 - - + +
32H LEU* 4.5 14.1 - - + -
33H LYS* 4.0 25.8 - - + +
47H ILE* 4.0 21.1 - - + -
49H GLU 3.4 4.3 + - - +
50H GLN* 3.2 38.3 + - - +
52H VAL* 1.3 75.6 - - - +
54H ASP* 1.3 70.7 + - - +
56H VAL* 4.3 5.4 - - + +
57H MET* 3.0 23.6 + - - +
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Residues in contact with ASP 54 (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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29H LYS* 2.6 37.9 + - - +
50H GLN* 2.8 53.5 + - - +
51H GLU* 3.7 9.1 + - - +
53H VAL* 1.3 71.9 - - - +
55H LYS* 1.3 58.5 + - - +
57H MET* 3.4 1.7 + - - +
58H GLU* 2.8 30.5 + - - +
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Residues in contact with LYS 55 (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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51H GLU 2.9 17.5 + - - +
52H VAL* 3.6 7.0 - - - +
53H VAL 3.2 0.2 - - - -
54H ASP* 1.3 75.4 - - - +
56H VAL* 1.3 64.8 + - + +
58H GLU* 3.4 23.3 + - - +
59H THR* 3.1 41.2 + - - -
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Residues in contact with VAL 56 (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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32H LEU* 4.0 19.1 - - + -
36H ILE* 4.2 15.7 - - + -
47H ILE* 4.7 11.4 - - + -
52H VAL* 3.0 26.3 + - + +
53H VAL* 3.3 8.9 + - + +
55H LYS* 1.3 76.4 - - + +
57H MET* 1.3 64.0 + - - +
59H THR* 3.2 8.3 + - - -
60H LEU* 3.0 39.2 + - + +
76H PHE* 4.4 9.2 - - + -
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Residues in contact with MET 57 (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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27H LEU 3.4 24.5 - - - +
28H LYS 3.8 1.6 - - - -
29H LYS* 3.6 39.3 - - + +
32H LEU* 3.9 19.5 - - + +
53H VAL 3.0 16.8 + - - +
54H ASP 3.8 2.7 - - - +
56H VAL* 1.3 76.5 - - - +
58H GLU* 1.3 58.1 + - - +
60H LEU* 4.4 3.4 - - - +
61H ASP* 2.7 45.1 + - + +
66H GLY* 3.6 23.6 - - - +
67H GLU 3.7 21.5 - - - +
68H CYS* 3.8 9.6 - - + +
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Residues in contact with GLU 58 (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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54H ASP 2.8 22.0 + - - +
55H LYS* 3.6 30.3 + - - +
56H VAL 3.3 0.2 - - - -
57H MET* 1.3 72.6 - - - +
59H THR* 1.3 66.2 + - - +
61H ASP* 3.6 15.1 + - - +
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Residues in contact with THR 59 (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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55H LYS* 3.1 25.3 + - - -
56H VAL* 3.5 10.3 - - - -
57H MET 3.2 0.2 - - - -
58H GLU* 1.3 82.7 - - - +
60H LEU* 1.3 62.9 + - + +
61H ASP 3.5 0.2 + - - -
62H ASN* 3.6 13.7 + - - +
79H MET* 4.2 24.1 - - + +
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Residues in contact with LEU 60 (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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32H LEU* 4.1 16.4 - - + -
56H VAL* 3.0 29.6 + - + +
57H MET* 3.9 6.5 - - - +
59H THR* 1.3 77.6 - - + +
61H ASP* 1.3 58.9 + - - +
62H ASN* 3.0 15.8 + - - +
68H CYS* 4.1 21.8 - - - -
72H GLU* 3.4 25.0 - - - +
75H ALA* 6.0 0.6 - - + +
76H PHE* 3.6 45.1 - - + +
79H MET* 3.2 34.5 - - + -
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Residues in contact with ASP 61 (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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57H MET* 2.7 30.4 + - + +
58H GLU* 3.6 10.8 + - - +
59H THR 3.4 2.0 - - - -
60H LEU* 1.3 70.5 - - - +
62H ASN* 1.3 59.8 + - - +
63H ASP* 3.0 8.5 - - - +
64H GLY* 3.1 14.9 + - - -
65H ASP* 3.2 4.2 + - - +
66H GLY* 2.7 30.9 + - - -
67H GLU 3.7 7.4 - - - +
72H GLU* 3.9 4.0 - - - -
816H CA 2.2 30.7 - - - -
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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