Contacts of the helix formed by residues 74 - 83 (chain A) in PDB entry 4OIN
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A SER 4.2 4.0 - - - +
67A THR* 4.0 19.5 - - + +
72A LYS 3.6 3.0 + - - -
73A GLU* 1.3 77.9 - - - +
75A VAL* 1.3 61.4 + - - +
76A VAL* 3.1 17.2 + - - +
77A GLU* 2.9 36.3 + - - +
78A ILE* 2.9 25.9 + - - +
627C ARG* 3.3 31.8 + - - +
628C PHE* 4.4 9.4 - - + -
638C ASP* 5.4 0.2 - - - -
640C ARG* 3.7 15.6 + - - +
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Residues in contact with VAL 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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58A ILE* 4.3 17.0 - - + -
61A VAL* 3.9 28.9 - - + -
64A GLU* 3.3 32.1 + - - +
66A SER 3.2 19.1 + - - +
67A THR* 4.9 0.2 - - - -
68A ILE* 4.4 10.5 - - + -
74A ASP* 1.3 72.2 - - - +
76A VAL* 1.3 59.9 + - - +
78A ILE* 3.5 6.2 - - + +
79A ILE* 2.9 44.5 + - + +
165A ILE* 3.8 11.9 - - + -
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Residues in contact with VAL 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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64A GLU* 3.4 44.4 + - + +
65A PHE* 4.8 4.3 - - + -
74A ASP* 3.1 11.3 + - - +
75A VAL* 1.3 76.5 - - - +
77A GLU* 1.3 57.6 + - - +
79A ILE* 3.8 2.6 - - - +
80A LEU* 2.9 35.8 + - + +
572C ILE* 4.4 33.0 - - + -
628C PHE* 4.5 9.2 - - + -
703C ILE* 4.5 18.4 - - + -
830C LYS* 5.2 3.1 - - + -
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Residues in contact with GLU 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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73A GLU* 3.5 34.1 - - + +
74A ASP* 2.9 27.8 + - - +
75A VAL 3.2 0.2 - - - -
76A VAL* 1.3 76.1 - - - +
78A ILE* 1.3 60.2 + - - +
80A LEU* 3.1 13.1 + - + +
81A ASN* 2.9 45.0 + - - +
640C ARG* 5.4 3.3 - - - +
642C ARG* 5.1 12.0 + - - -
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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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58A ILE* 4.2 11.9 - - + -
68A ILE* 4.3 19.7 - - + -
71A VAL* 4.2 14.4 - - + -
73A GLU* 4.0 22.0 - - + +
74A ASP 2.9 20.7 + - - +
75A VAL* 3.5 11.4 - - - +
77A GLU* 1.3 75.9 - - - +
79A ILE* 1.3 58.8 + - + +
81A ASN* 3.3 9.2 + - - +
82A LEU* 2.9 45.1 + - + +
129A ILE* 4.3 14.7 - - + +
130A ALA* 4.6 6.7 - - + -
138A LEU* 4.8 5.8 - - + -
140A MET* 4.1 14.6 - - - -
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Residues in contact with ILE 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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56A VAL* 4.6 16.4 - - + -
64A GLU* 3.6 39.0 - - + +
75A VAL* 2.9 27.7 + - + +
76A VAL 3.8 3.6 - - - +
78A ILE* 1.3 73.8 - - + +
80A LEU* 1.3 62.5 + - + +
82A LEU* 3.2 7.7 + - + -
83A LYS* 2.9 30.5 + - + +
165A ILE* 3.7 24.2 - - + -
166A PRO 5.3 0.4 - - - +
167A VAL* 3.6 34.7 - - + +
168A ASP 5.6 0.2 - - - +
830C LYS* 5.8 1.3 - - - +
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Residues in contact with LEU 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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76A VAL* 2.9 36.1 + - + +
77A GLU* 3.1 15.2 + - + +
79A ILE* 1.3 79.1 - - + +
81A ASN* 1.3 64.7 + - - +
83A LYS* 3.5 29.1 + - - +
84A GLU* 3.8 12.8 - - - +
572C ILE* 4.7 7.6 - - + +
573C ARG* 4.0 36.8 - - + +
698C ASP* 3.8 29.8 - - + +
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Residues in contact with ASN 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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73A GLU* 4.3 3.8 - - - +
77A GLU* 2.9 35.8 + - - +
78A ILE 3.6 6.5 - - - +
80A LEU* 1.3 76.7 - - - +
82A LEU* 1.3 57.8 + - - +
83A LYS 3.0 4.5 - - - -
84A GLU* 3.0 28.2 + - - +
127A LEU* 3.5 14.0 - - + +
128A HIS* 3.5 30.2 + - - +
129A ILE* 3.1 28.7 + - - +
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Residues in contact with LEU 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 VAL* 3.3 22.2 + - + +
56A VAL* 3.6 33.7 - - + -
78A ILE* 2.9 38.1 + - + +
79A ILE* 3.2 7.6 + - + +
81A ASN* 1.3 75.7 - - - +
83A LYS* 1.3 56.7 + - - +
84A GLU 3.1 1.1 - - - -
85A LEU* 3.2 30.5 + - + +
114A PHE* 3.8 25.4 - - + -
129A ILE* 3.6 24.7 - - + -
140A MET* 4.1 9.0 - - + -
142A VAL* 3.9 12.3 - - + -
167A VAL* 5.8 0.2 - - - -
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Residues in contact with LYS 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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52A ALA* 6.0 2.4 - - - +
53A VAL* 5.2 3.6 - - - +
79A ILE* 2.9 17.3 + - + +
80A LEU* 3.5 25.1 - - + +
81A ASN 3.0 0.6 - - - -
82A LEU* 1.3 78.6 - - - +
84A GLU* 1.3 62.8 + - + +
85A LEU 3.3 4.4 + - - +
167A VAL* 4.5 10.8 - - + -
168A ASP* 3.3 41.8 + - + +
170A VAL* 5.4 11.6 - - + +
573C ARG* 6.2 0.4 - - - +
695C LEU 5.0 0.4 + - - -
696C LYS 3.4 24.8 + - - +
697C ARG* 4.5 3.3 - - - +
698C ASP* 2.7 32.5 + - - +
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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