Contacts of the helix formed by residues 78 - 87 (chain L) in PDB entry 2IAN
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 TYR 78 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7K ILE* 5.8 0.6 - - + +
9K GLN* 2.6 38.2 + - - +
24K PHE* 3.6 5.7 - + - -
13L PHE* 3.5 7.9 + - + +
15L CYS* 3.5 23.8 - - - -
26L LEU* 4.1 7.0 - - + -
74L ALA* 2.8 20.1 + - + +
76L ASP 3.1 0.6 - - - -
77L THR* 1.3 81.7 + - - +
79L CYS* 1.3 71.7 + - - +
81L HIS* 4.0 2.5 - - - -
82L ASN* 3.0 42.9 + - - +
27M GLY* 3.1 31.0 - - - -
28M THR 3.9 2.9 - - - -
29M LEU* 3.4 47.8 - - + -
91N GLN* 5.4 1.1 - - - -
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Residues in contact with CYS 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L CYS* 2.1 55.0 - - + -
17L PHE* 3.8 6.9 - - + -
24L VAL* 3.5 21.1 - - + -
26L LEU* 4.1 19.5 - - - -
74L ALA 2.8 17.0 + - - -
75L VAL* 3.3 12.3 - - - +
78L TYR* 1.3 71.4 - - - +
80L ARG* 1.3 66.9 + - - +
81L HIS 2.9 2.2 + - - -
82L ASN* 3.0 5.1 + - - +
83L TYR* 2.9 22.7 + - - +
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Residues in contact with ARG 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L PHE* 4.7 0.4 - - - -
21L THR* 3.0 37.7 + - + +
22L GLU 3.1 26.1 + - - -
23L ARG* 4.4 0.2 - - - +
24L VAL* 3.3 26.1 + - + +
75L VAL* 3.1 36.1 + - - +
76L ASP* 2.9 42.2 + - - +
79L CYS* 1.3 76.4 - - - +
81L HIS* 1.3 63.7 + - - +
83L TYR* 3.6 9.4 - - - +
84L GLY* 3.3 14.9 + - - -
65N THR* 4.7 10.8 - - - +
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Residues in contact with HIS 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ASP 3.2 10.5 + - - +
77L THR* 3.5 20.0 - - - +
78L TYR 3.8 1.8 - - - +
79L CYS 2.9 1.4 + - - -
80L ARG* 1.3 76.1 - - - +
82L ASN* 1.3 77.8 + - - +
84L GLY* 2.8 23.0 + - - -
85L VAL* 3.2 20.7 + - + +
24M GLU* 4.5 3.1 - - + -
25M LEU 2.8 26.9 + - - -
27M GLY* 4.0 2.4 + - - -
26N ASP* 3.1 31.0 + - + -
29N ASN* 5.0 5.2 + - - +
67N ARG* 5.9 2.8 - - - -
91N GLN* 3.5 32.0 + - + +
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Residues in contact with ASN 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ILE* 4.2 21.5 - - + +
24K PHE* 3.8 13.7 - - - -
15L CYS* 6.0 1.3 - - - -
78L TYR* 3.0 32.6 + - - +
79L CYS* 3.0 4.7 + - - +
81L HIS* 1.3 84.0 - - - +
83L TYR* 1.3 65.1 + - - +
85L VAL* 3.4 6.7 + - - +
86L GLY* 3.1 21.0 + - - -
26M ILE* 3.4 14.1 - - + +
27M GLY* 2.6 48.2 + - - -
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Residues in contact with TYR 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K GLU* 5.1 1.0 + - - -
5K HIS* 4.4 10.9 - + + -
7K ILE* 4.1 10.6 - - + +
26K PHE* 5.7 0.7 - + - -
17L PHE* 3.7 47.3 - + + -
20L GLY* 3.9 23.7 - - - -
21L THR* 3.4 24.5 - - + -
79L CYS 2.9 13.1 + - - +
80L ARG 3.6 10.3 - - - +
82L ASN* 1.3 75.6 - - - +
84L GLY* 1.3 55.0 + - - +
87L GLU* 2.8 59.8 + - - +
91L VAL* 3.5 38.2 - - + +
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Residues in contact with GLY 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L ARG 3.3 6.7 + - - -
81L HIS 2.8 9.9 + - - -
83L TYR* 1.3 80.6 - - - +
85L VAL* 1.3 63.8 + - - +
87L GLU* 3.7 20.7 - - - +
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Residues in contact with VAL 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K PHE 4.5 4.9 - - - +
52K ALA* 3.6 20.9 - - + -
81L HIS* 3.5 26.2 - - + +
82L ASN* 3.7 9.4 - - - +
84L GLY* 1.3 80.0 - - - +
86L GLY* 1.3 61.3 + - - +
88L SER* 4.5 4.0 + - - -
89L PHE* 3.3 14.9 - - - -
24M GLU* 4.0 27.8 - - + +
25M LEU 3.6 20.0 - - - +
26M ILE* 3.6 26.5 - - + -
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Residues in contact with GLY 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ILE* 6.1 2.0 - - - -
82L ASN 3.1 14.9 + - - -
85L VAL* 1.3 76.2 - - - +
87L GLU* 1.3 67.2 + - - +
88L SER 2.8 3.3 + - - -
89L PHE* 3.0 34.7 + - - -
90L THR* 3.1 19.1 + - - -
26M ILE* 5.9 2.2 - - - -
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Residues in contact with GLU 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L TYR* 2.8 42.4 + - + +
84L GLY* 3.7 21.0 - - - +
86L GLY* 1.3 69.2 - - - +
88L SER* 1.3 60.6 + - - +
90L THR* 3.5 5.4 + - - -
91L VAL* 3.0 20.0 + - + +
92L GLN* 2.7 63.2 + - + +
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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