Contacts of the helix formed by residues 79 - 94 (chain T) in PDB entry 1IR1
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 79 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34T LEU* 3.7 2.7 - - - -
77T CYS* 3.4 7.9 - - - -
78T THR* 1.3 82.4 + - - +
80T PRO* 1.3 73.1 - - - +
81T ALA* 3.2 26.5 + - - +
82T GLN* 3.0 45.9 + - - +
83T VAL 3.8 0.3 + - - -
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Residues in contact with PRO 80 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27T ALA* 5.0 2.9 - - + +
30T VAL* 3.9 19.5 - - + -
31T ASP* 3.1 29.2 - - - +
34T LEU* 3.3 19.0 - - + -
78T THR 3.7 4.7 - - - +
79T ASP* 1.3 88.7 - - - +
81T ALA* 1.3 63.5 + - + +
82T GLN 3.1 0.2 - - - -
83T VAL* 3.2 4.9 + - + +
84T LEU* 3.1 32.5 + - + +
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Residues in contact with ALA 81 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79T ASP* 3.1 21.9 - - - +
80T PRO* 1.3 81.9 - - + +
82T GLN* 1.3 54.5 + - - +
84T LEU* 3.5 11.2 + - - +
85T ASN* 2.9 37.8 + - - +
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Residues in contact with GLN 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74T MET* 3.6 22.5 - - + +
77T CYS* 3.3 30.3 - - - +
78T THR 4.6 0.2 - - - +
79T ASP* 3.0 32.5 + - - +
81T ALA* 1.3 79.9 - - - +
83T VAL* 1.3 60.6 + - - +
85T ASN* 3.5 7.5 + - - +
86T GLU* 3.3 18.9 + - - +
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Residues in contact with VAL 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T VAL* 4.0 25.8 - - + -
34T LEU* 4.8 2.7 - - + -
40T PRO* 3.9 26.5 - - + -
42T LEU* 4.3 19.6 - - + +
74T MET* 4.1 10.1 - - - -
77T CYS* 3.9 23.1 - - - -
79T ASP 4.3 2.2 - - - +
80T PRO* 3.6 7.6 - - + +
82T GLN* 1.3 76.5 - - - +
84T LEU* 1.3 65.6 + - - +
86T GLU* 3.2 5.0 + - - +
87T LEU* 3.1 20.1 + - - +
101T ILE* 4.6 19.3 - - + -
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Residues in contact with LEU 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T THR* 5.6 4.3 - - + +
26T LEU* 5.1 15.5 - - + -
27T ALA* 4.4 24.0 - - + +
30T VAL* 3.7 30.7 - - + -
80T PRO* 3.1 23.6 + - + +
81T ALA* 3.8 10.3 - - - +
83T VAL* 1.3 78.2 - - + +
85T ASN* 1.3 62.8 + - - +
87T LEU* 3.4 12.9 - - + +
88T GLU* 3.2 26.2 + - - +
101T ILE* 5.8 0.9 - - + -
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Residues in contact with ASN 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T ALA* 2.9 23.7 + - - +
82T GLN* 3.6 9.3 - - - +
83T VAL 3.1 0.2 - - - -
84T LEU* 1.3 75.0 - - - +
86T GLU* 1.3 67.5 + - + +
88T GLU* 3.1 11.6 + - - +
89T GLU* 3.0 26.1 + - - +
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Residues in contact with GLU 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T LEU* 3.7 13.4 - - + +
70T TRP* 2.8 32.3 + - + +
71T LYS* 3.0 30.8 + - - +
74T MET* 4.0 20.4 - - + +
82T GLN 3.3 12.7 + - - +
83T VAL 3.2 9.0 + - - +
85T ASN* 1.3 78.3 - - + +
87T LEU* 1.3 60.5 + - - +
89T GLU* 3.1 14.1 + - - +
90T CYS* 2.8 32.6 + - - +
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Residues in contact with LEU 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T LEU* 4.0 22.4 - - + -
42T LEU* 3.6 12.3 - - + +
83T VAL 3.1 12.5 + - - +
84T LEU* 3.4 17.0 - - + +
85T ASN 3.1 0.2 - - - -
86T GLU* 1.3 77.0 - - - +
88T GLU* 1.3 63.6 + - - +
90T CYS* 3.3 1.2 + - - +
91T LYS* 2.9 53.0 + - + +
99T ILE* 3.7 29.4 - - + -
101T ILE* 4.4 11.9 - - + -
117T ALA* 4.0 29.2 - - + +
118T TYR* 4.7 1.8 - - + -
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Residues in contact with GLU 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T LEU 3.2 12.7 + - - +
85T ASN* 3.1 13.1 + - - +
87T LEU* 1.3 86.3 - - - +
89T GLU* 1.3 63.0 + - - +
91T LYS* 3.1 36.1 + - - +
92T LYS* 3.0 24.1 + - - +
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Residues in contact with GLU 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T TRP* 3.8 15.9 - - + -
71T LYS* 3.4 28.6 + - - -
85T ASN* 3.0 16.8 + - - +
86T GLU* 3.4 18.1 - - - +
88T GLU* 1.3 77.4 - - - +
90T CYS* 1.3 64.1 + - - +
92T LYS* 3.2 17.3 + - - +
93T GLU* 3.2 21.8 + - - +
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Residues in contact with CYS 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T LEU* 4.2 8.3 - - + -
43T GLU 5.6 0.2 - - - -
44T PHE* 4.2 20.4 - - - -
70T TRP* 3.7 41.0 - - + -
86T GLU 2.8 19.5 + - - +
87T LEU 3.6 4.3 - - - +
89T GLU* 1.3 74.0 - - - +
91T LYS* 1.3 53.0 + - - +
93T GLU* 3.2 2.1 + - - +
94T TYR* 2.8 36.8 + - - +
99T ILE* 3.7 28.5 - - + -
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Residues in contact with LYS 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87T LEU* 2.9 34.9 + - + +
88T GLU* 3.1 36.5 + - - +
90T CYS* 1.3 76.0 - - - +
92T LYS* 1.3 61.5 + - - +
94T TYR 4.3 2.2 - - - -
95T PRO* 3.1 29.0 - - - +
99T ILE* 3.5 22.4 - - + +
117T ALA 5.8 0.2 - - - +
118T TYR* 3.6 36.7 + - + -
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Residues in contact with LYS 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88T GLU 3.0 17.7 + - - +
89T GLU* 3.5 15.5 + - - +
90T CYS 3.2 0.4 - - - -
91T LYS* 1.3 80.2 - - - +
93T GLU* 1.3 61.2 + - - +
95T PRO* 3.8 8.7 - - - +
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Residues in contact with GLU 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T TRP* 2.9 28.8 - - + -
89T GLU 3.2 14.3 + - - +
90T CYS 3.9 0.7 - - - +
92T LYS* 1.3 81.4 - - - +
94T TYR* 1.3 88.6 + - + +
95T PRO* 3.6 5.3 - - - +
96T ASN* 5.0 0.7 - - - +
3U VAL* 4.3 18.3 + - - +
5U PRO* 5.6 3.6 - - - +
7U GLN* 5.4 1.0 - - - +
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Residues in contact with TYR 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T PHE* 3.5 40.8 - + + -
46T THR* 4.0 13.7 - - + -
70T TRP* 4.1 11.9 - + - -
90T CYS* 2.8 18.9 + - - +
91T LYS* 3.4 6.2 - - - +
93T GLU* 1.3 113.8 + - + +
95T PRO* 1.3 61.8 - - - +
96T ASN* 3.1 9.6 + - - -
97T ALA* 3.2 24.8 + - + +
99T ILE* 4.4 2.5 - - + +
118T TYR* 4.1 4.2 - - - -
3U VAL* 4.8 3.6 + - + +
4U TRP 4.2 2.1 + - - -
5U PRO* 3.5 29.3 - - - +
6U THR* 3.6 14.3 + - - -
7U GLN* 3.9 22.9 - - + -
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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