Contacts of the helix formed by residues 74 - 83 (chain A) in PDB entry 2E34
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 ALA 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PRO* 1.3 71.5 - - + +
75A SER* 1.3 57.2 + - - +
76A TYR* 2.5 46.0 + - - -
78A ILE* 2.8 41.4 + - + +
111A LYS* 6.3 0.8 - - - +
127A ILE* 5.0 6.5 - - + -
130A SER* 3.8 20.9 - - - +
134A MET* 5.2 2.7 - - + -
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS 2.7 1.7 - - - +
71A THR* 2.2 42.4 + - - -
72A PRO* 3.3 11.4 - - - -
73A PRO 2.2 17.0 + - - -
74A ALA* 1.3 70.8 - - - +
76A TYR* 1.3 61.3 + - - -
77A LEU 2.7 2.0 + - - -
78A ILE* 3.5 13.2 - - - +
79A ARG* 2.2 57.8 + - - +
134A MET* 3.5 9.7 - - - +
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PRO* 5.5 3.4 - - + -
68A VAL 5.2 0.9 - - - +
69A THR* 3.4 26.8 - - - +
70A LYS* 2.7 34.4 + - - +
71A THR 3.3 5.4 - - - +
72A PRO 2.8 8.4 + - - +
73A PRO* 4.0 2.9 - - + -
74A ALA* 2.5 53.7 + - - +
75A SER* 1.3 73.1 - - - +
77A LEU* 1.3 102.0 + - + +
79A ARG* 5.3 0.2 - - - +
107A ILE* 3.5 20.4 + - + +
111A LYS* 5.7 4.5 - - + +
127A ILE* 5.1 4.2 - - + +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA 2.9 3.7 + - - +
75A SER 3.6 0.2 - - - -
76A TYR* 1.3 129.2 - - + +
78A ILE* 1.3 89.1 + - + +
79A ARG 3.0 2.5 - - - -
80A LYS* 2.9 21.6 + - + +
81A ALA* 3.2 10.0 + - - +
107A ILE* 3.4 40.8 - - + -
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA* 2.8 49.7 + - + +
75A SER* 3.5 0.7 - - - -
77A LEU* 1.3 91.5 - - + +
79A ARG* 1.3 51.1 + - - +
81A ALA* 3.2 2.3 + - - +
82A ALA* 2.5 41.9 + - + +
99A ILE* 4.3 10.5 - - + -
107A ILE* 4.5 7.2 - - + -
127A ILE* 3.1 46.2 - - + +
130A SER* 3.5 1.8 - - - +
131A ALA* 4.2 16.2 - - + +
134A MET* 3.5 20.0 - - + -
136A VAL* 4.6 0.2 - - + -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 4.8 3.8 - - + +
71A THR* 3.2 27.8 - - + +
72A PRO* 4.6 9.5 - - - +
75A SER* 2.2 60.8 + - - +
76A TYR 5.3 0.4 - - - +
77A LEU* 3.0 0.6 - - - -
78A ILE* 1.3 79.0 - - - +
80A LYS* 1.3 65.6 + - - +
82A ALA* 2.8 21.6 + - - +
83A GLY 3.3 4.3 + - - -
84A LEU* 3.2 43.5 + - + +
134A MET* 2.5 42.8 - - - +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 2.9 16.8 + - + +
79A ARG* 1.3 77.7 - - - +
81A ALA* 1.3 62.8 + - + +
82A ALA* 2.6 15.7 + - - -
83A GLY* 3.8 5.4 + - - -
84A LEU* 4.6 7.8 + - - +
103A GLN* 5.3 8.3 - - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU 3.2 4.0 + - - +
78A ILE 3.9 2.0 - - - +
80A LYS* 1.3 87.0 - - + +
82A ALA* 1.3 56.8 + - - +
98A ARG 2.8 16.3 - - - +
99A ILE* 2.9 28.5 - - + +
100A THR* 5.4 0.3 - - - +
103A GLN* 3.8 26.9 - - + +
107A ILE* 3.8 25.8 - - + -
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE 2.5 18.9 + - - +
79A ARG* 2.8 18.8 - - - +
80A LYS 2.6 6.0 + - - -
81A ALA* 1.3 70.5 - - - +
83A GLY* 1.3 57.8 + - - +
84A LEU* 4.9 2.9 - - + -
97A GLY* 3.6 18.2 - - - -
98A ARG* 2.1 46.6 + - - +
99A ILE* 3.8 2.7 - - - -
134A MET* 5.4 0.2 - - - -
136A VAL* 4.2 13.2 - - + -
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG 3.3 0.8 + - - -
80A LYS 3.8 2.2 + - - -
82A ALA* 1.3 83.2 - - - +
84A LEU* 1.3 70.9 + - - +
85A GLU* 3.3 7.0 + - - +
95A LYS 4.3 3.1 - - - +
96A VAL* 3.2 25.0 - - - +
97A GLY 3.5 10.1 - - - +
98A ARG* 4.1 1.1 - - - -
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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