Contacts of the helix formed by residues 79 - 94 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34U LEU* 3.9 3.1 - - - -
77U CYS* 3.6 8.2 - - - -
78U THR* 1.3 82.8 + - - +
80U PRO* 1.3 66.3 - - - +
81U ALA* 3.1 30.4 + - - +
82U GLN* 2.9 40.7 + - + +
83U VAL 3.7 0.9 + - - -
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Residues in contact with PRO 80 (chain U).
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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27U ALA* 5.1 3.1 - - + +
30U VAL* 3.8 22.4 - - + +
31U ASP* 3.9 26.2 - - - +
34U LEU* 3.5 17.4 - - + -
78U THR 3.7 7.6 - - - +
79U ASP* 1.3 89.6 - - - +
81U ALA* 1.3 62.3 + - - +
83U VAL* 3.0 6.9 + - + +
84U LEU* 3.0 31.1 + - + +
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Residues in contact with ALA 81 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79U ASP* 3.1 21.2 + - - +
80U PRO* 1.3 79.6 - - - +
82U GLN* 1.3 52.2 + - - +
84U LEU* 3.3 10.3 + - - +
85U ASN* 2.8 47.4 + - - +
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Residues in contact with GLN 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74U MET* 3.2 35.0 - - + +
77U CYS* 3.6 24.3 - - - +
78U THR 4.6 0.7 + - - -
79U ASP* 2.9 29.0 + - + +
81U ALA* 1.3 80.7 - - - +
83U VAL* 1.3 58.7 + - - +
85U ASN* 3.3 9.1 - - + +
86U GLU* 3.2 19.4 + - + +
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Residues in contact with VAL 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30U VAL* 4.0 31.0 - - + -
33U LEU* 6.2 0.2 - - + -
34U LEU* 4.5 2.5 - - + -
40U PRO* 3.9 36.3 - - + -
42U LEU* 4.6 15.3 - - + +
74U MET* 4.2 8.3 - - - -
77U CYS* 4.0 15.7 - - - -
79U ASP 4.2 2.0 - - - +
80U PRO* 3.0 10.0 + - + +
82U GLN* 1.3 73.6 - - - +
84U LEU* 1.3 61.9 + - - +
85U ASN 3.0 4.0 - - - -
86U GLU* 3.2 5.0 + - - +
87U LEU* 3.1 20.6 + - - +
101U ILE* 4.6 16.2 - - + -
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Residues in contact with LEU 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U THR* 5.8 2.0 - - + +
26U LEU* 4.1 32.5 - - + -
27U ALA* 4.3 24.2 - - + -
30U VAL* 4.2 16.8 - - + -
80U PRO* 3.0 22.7 + - + +
81U ALA* 3.6 7.4 - - - +
83U VAL* 1.3 76.1 - - - +
85U ASN* 1.3 60.8 + - - +
87U LEU* 3.6 15.0 + - + +
88U GLU* 3.3 27.5 + - - +
101U ILE* 5.3 2.5 - - + -
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Residues in contact with ASN 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81U ALA* 2.8 28.1 + - - +
82U GLN* 3.3 11.2 - - - +
83U VAL 3.0 0.4 - - - -
84U LEU* 1.3 76.6 - - - +
86U GLU* 1.3 66.6 + - + +
88U GLU* 3.3 8.3 + - - +
89U GLU* 3.2 27.5 + - + +
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Residues in contact with GLU 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U LEU* 3.8 14.8 - - + -
70U TRP* 2.8 35.9 + - + +
71U LYS* 2.9 29.6 + - - +
74U MET* 4.0 20.0 - - + +
82U GLN* 3.2 11.9 + - + +
83U VAL 3.2 8.8 + - - +
85U ASN* 1.3 79.0 - - - +
87U LEU* 1.3 61.3 + - - +
89U GLU* 3.1 12.3 + - - +
90U CYS* 2.8 31.4 + - - +
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Residues in contact with LEU 87 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U LEU* 4.2 24.7 - - + -
42U LEU* 3.5 13.4 - - + +
83U VAL 3.1 13.2 + - - +
84U LEU* 3.6 20.0 - - + +
85U ASN 3.2 0.2 - - - -
86U GLU* 1.3 77.6 - - - +
88U GLU* 1.3 63.8 + - - +
90U CYS* 3.3 1.9 + - - +
91U LYS* 3.0 52.1 + - + +
99U ILE* 3.8 28.5 - - + -
101U ILE* 4.6 7.6 - - + -
117U ALA* 4.2 25.4 - - + +
118U TYR* 4.7 2.9 - - + -
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Residues in contact with GLU 88 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84U LEU 3.3 14.6 + - - +
85U ASN* 3.3 9.5 + - - +
86U GLU 3.3 0.2 - - - -
87U LEU* 1.3 79.1 - - - +
89U GLU* 1.3 66.3 + - - +
91U LYS* 3.1 37.6 + - - +
92U LYS* 3.0 40.0 + - + +
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Residues in contact with GLU 89 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U TRP* 3.9 13.7 - - + -
71U LYS* 3.2 25.1 + - - -
85U ASN* 3.2 17.2 + - - +
86U GLU* 3.1 17.3 + - - +
88U GLU* 1.3 81.1 - - - +
90U CYS* 1.3 61.7 + - - +
92U LYS* 3.3 8.9 + - - +
93U GLU* 3.2 22.0 + - - +
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Residues in contact with CYS 90 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U LEU* 4.5 4.0 - - + -
44U PHE* 4.2 18.6 - - - -
70U TRP* 3.7 42.6 - - + -
86U GLU 2.8 16.2 + - - +
87U LEU* 3.6 7.6 - - - +
88U GLU 3.2 0.2 - - - -
89U GLU* 1.3 78.5 - - - +
91U LYS* 1.3 56.0 + - - +
93U GLU* 3.4 1.2 + - - +
94U TYR* 2.8 31.9 + - - +
99U ILE* 3.6 29.4 - - + -
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Residues in contact with LYS 91 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87U LEU* 3.0 36.2 + - + +
88U GLU* 3.1 40.2 + - - +
90U CYS* 1.3 73.6 - - - +
92U LYS* 1.3 69.5 + - + +
94U TYR 4.2 3.1 - - - -
95U PRO* 3.1 28.5 - - - +
99U ILE* 3.6 20.9 - - + -
117U ALA 6.0 0.4 + - - -
118U TYR* 3.7 36.6 - - + -
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Residues in contact with LYS 92 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88U GLU* 3.0 27.5 + - + +
89U GLU* 3.4 11.9 - - - +
91U LYS* 1.3 81.8 - - + +
93U GLU* 1.3 59.7 + - - +
95U PRO* 3.7 8.1 - - - +
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Residues in contact with GLU 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U TRP* 3.3 27.4 - - + -
89U GLU 3.2 12.0 + - - +
90U CYS 4.1 0.9 - - - +
92U LYS* 1.3 79.8 - - - +
94U TYR* 1.3 86.7 + - + +
95U PRO* 3.5 5.7 - - - +
96U ASN* 4.9 0.5 - - - +
3V VAL* 4.2 15.2 + - - +
7V GLN* 5.5 0.5 - - - +
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Residues in contact with TYR 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U PHE* 3.6 38.8 - + + -
46U THR* 4.0 17.9 - - + -
70U TRP* 4.1 10.3 - + - -
90U CYS* 2.8 19.5 + - - +
91U LYS* 3.4 6.4 - - - +
93U GLU* 1.3 113.5 + - + +
95U PRO* 1.3 61.2 - - - +
96U ASN* 3.1 9.2 + - - -
97U ALA* 3.2 24.8 + - + +
99U ILE* 4.4 2.6 - - + +
118U TYR* 4.2 3.6 - - - -
3V VAL* 4.9 3.6 + - + +
4V TRP 4.2 1.7 + - - -
5V PRO* 3.3 30.8 - - - +
6V THR* 3.6 13.5 + - - -
7V GLN* 3.9 19.3 - - + -
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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