Contacts of the helix formed by residues 79 - 86 (chain A) in PDB entry 3REZ
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 ARG 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLU 3.4 0.4 - - - -
78A ASP* 1.3 102.3 + - - +
80A PRO* 1.4 77.1 - - + +
81A GLU* 4.2 21.9 + - + +
82A ARG* 3.2 56.8 + - + +
86A ARG* 3.3 14.3 + - - -
83D ALA* 3.2 42.4 + - + +
84D PRO* 4.5 2.8 - - - +
86D ARG* 3.8 11.7 - - - +
87D ASP* 3.0 32.5 + - - -
103D TYR* 3.1 9.7 + - - -
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Residues in contact with PRO 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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78A ASP 4.8 0.4 - - - +
79A ARG* 1.4 89.3 - - + +
81A GLU* 1.3 56.6 + - - +
82A ARG 3.1 0.4 - - - -
83A ALA* 3.0 29.7 + - + +
84A PRO* 4.1 1.7 - - - +
86A ARG* 4.4 6.1 - - - +
80C PRO* 4.4 28.7 - - + -
80D PRO* 4.4 27.8 - - + -
83D ALA* 6.1 0.2 - - + -
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Residues in contact with GLU 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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54A ARG* 3.0 57.5 + - - +
79A ARG* 4.2 26.2 + - + -
80A PRO* 1.3 78.3 - - - +
82A ARG* 1.3 65.6 + - + +
83A ALA 3.4 0.7 - - - -
84A PRO* 3.5 13.2 - - - +
85A TYR* 3.7 13.0 - - - -
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Residues in contact with ARG 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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53A LEU 4.0 11.1 + - - -
54A ARG* 4.3 14.7 + - - +
55A THR* 6.0 0.4 - - - -
75A TRP* 2.8 84.4 + - + +
76A LEU* 3.5 21.3 - - + +
78A ASP* 4.1 1.4 - - - +
79A ARG* 3.2 47.8 + - + +
80A PRO 3.1 1.2 - - - -
81A GLU* 1.3 80.6 + - + +
83A ALA* 1.3 64.5 + - - +
84A PRO* 3.3 3.6 - - - -
85A TYR* 3.1 22.6 + - + +
86A ARG* 3.3 11.8 + - - +
87D ASP* 5.1 2.2 + - - -
103D TYR* 3.0 31.7 + - - -
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Residues in contact with ALA 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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80A PRO* 3.0 17.5 + - + +
82A ARG* 1.3 77.2 - - - +
84A PRO* 1.4 65.3 - - + +
85A TYR 3.1 1.4 + - - -
86A ARG* 3.3 44.7 + - - +
87A ASP* 4.6 2.3 + - - +
79C ARG* 3.3 38.1 + - + +
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Residues in contact with PRO 84 (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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80A PRO 4.1 0.9 - - - +
81A GLU* 3.5 14.4 - - - +
82A ARG 3.4 4.7 - - - -
83A ALA* 1.4 93.0 - - + +
85A TYR* 1.3 80.0 + - + +
86A ARG 3.5 1.3 - - - -
87A ASP* 5.2 2.9 + - - +
79C ARG* 4.8 3.6 - - - +
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Residues in contact with TYR 85 (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 ARG 5.9 0.7 - - - -
55A THR* 3.8 27.4 + - + +
56A ALA 3.5 21.9 - - - +
57A HIS* 3.4 38.0 - + - -
58A LEU* 5.0 2.6 + - - +
76A LEU* 4.1 12.4 - - + +
81A GLU 3.7 21.3 - - - -
82A ARG* 3.1 17.3 + - + +
84A PRO* 1.3 96.2 - - + +
86A ARG* 1.3 60.9 + - - +
87A ASP 3.5 1.8 - - - -
88A LEU* 3.7 18.4 - - - +
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Residues in contact with ARG 86 (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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76A LEU* 3.1 41.0 + - + +
77A GLU* 3.2 43.7 + - - +
79A ARG 3.3 23.4 + - - -
80A PRO* 4.4 2.4 - - - +
82A ARG 3.4 7.2 - - - +
83A ALA* 3.3 35.9 + - - +
84A PRO 3.5 0.4 - - - -
85A TYR* 1.3 75.9 - - - +
87A ASP* 1.3 59.9 + - - +
88A LEU* 2.9 16.0 + - - +
101A LEU* 4.6 2.9 - - - +
102A PRO* 3.5 15.7 - - + +
78C ASP* 3.0 48.3 + - - -
79C ARG* 3.6 9.1 - - - +
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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