Contacts of the helix formed by residues 79 - 94 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34V LEU* 3.8 2.5 - - - -
77V CYS* 3.5 5.8 - - - -
78V THR* 1.3 82.2 + - - +
80V PRO* 1.3 72.9 - - - +
81V ALA* 3.2 28.3 + - - +
82V GLN* 2.9 44.2 + - + +
83V VAL 3.8 0.5 + - - -
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Residues in contact with PRO 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V ALA* 5.1 2.9 - - + +
30V VAL* 3.8 21.7 - - + +
31V ASP* 3.8 29.8 - - - +
34V LEU* 3.4 17.7 - - + -
78V THR 3.7 8.3 - - - +
79V ASP* 1.3 89.0 - - - +
81V ALA* 1.3 63.3 + - + +
82V GLN 3.2 0.2 - - - -
83V VAL* 3.2 6.5 + - + +
84V LEU* 3.2 32.3 + - + +
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Residues in contact with ALA 81 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V ASP* 3.0 25.3 + - - +
80V PRO* 1.3 80.6 - - + +
82V GLN* 1.3 61.4 + - - +
84V LEU* 3.6 8.0 + - - +
85V ASN* 3.0 39.1 + - - +
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Residues in contact with GLN 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74V MET* 3.6 16.8 - - + +
76V GLY 5.3 0.2 - - - +
77V CYS* 3.4 28.2 - - - +
78V THR* 4.0 5.4 + - - -
79V ASP* 2.9 39.2 + - + +
81V ALA* 1.3 78.5 - - - +
83V VAL* 1.3 60.5 + - - +
85V ASN* 3.5 6.5 + - - +
86V GLU* 3.2 27.4 + - - +
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Residues in contact with VAL 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V VAL* 4.0 33.2 - - + -
34V LEU* 4.6 2.2 - - + -
40V PRO* 3.9 33.4 - - + -
42V LEU* 4.3 20.1 - - + +
74V MET* 4.2 9.4 - - - -
77V CYS* 4.0 15.3 - - - -
79V ASP 4.2 2.5 - - - +
80V PRO* 3.2 7.8 + - + +
82V GLN* 1.3 72.5 - - - +
84V LEU* 1.3 66.0 + - - +
85V ASN 3.1 1.6 - - - -
86V GLU* 3.0 15.1 + - - +
87V LEU* 3.0 10.9 + - - +
101V ILE* 4.6 13.5 - - + -
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Residues in contact with LEU 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V LEU* 3.9 34.3 - - + -
27V ALA* 4.4 22.7 - - + -
30V VAL* 4.2 17.3 - - + -
80V PRO* 3.2 23.1 + - + +
81V ALA* 4.2 6.3 - - - +
83V VAL* 1.3 75.5 - - - +
85V ASN* 1.3 61.8 + - - +
87V LEU* 3.3 15.5 - - + +
88V GLU* 3.1 26.9 + - - +
101V ILE* 5.3 2.2 - - + -
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Residues in contact with ASN 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81V ALA* 3.0 32.1 + - - +
82V GLN* 3.5 8.7 - - - +
84V LEU* 1.3 75.6 - - - +
86V GLU* 1.3 66.7 + - + +
88V GLU* 3.2 10.3 + - - +
89V GLU* 3.0 22.2 + - - +
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Residues in contact with GLU 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V LEU* 3.8 12.1 - - + -
70V TRP* 2.9 34.3 + - + +
71V LYS* 3.0 31.7 + - - +
74V MET* 3.7 22.3 - - + +
82V GLN 3.2 12.9 + - - +
83V VAL* 3.0 9.2 + - - +
85V ASN* 1.3 76.3 - - - +
87V LEU* 1.3 61.8 + - - +
89V GLU* 3.1 10.3 + - - +
90V CYS* 2.8 31.0 + - - +
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Residues in contact with LEU 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V LEU* 4.0 26.9 - - + -
42V LEU* 3.6 11.8 - - + +
83V VAL 3.0 11.9 + - - +
84V LEU* 3.3 21.1 - - + +
86V GLU* 1.3 77.5 - - - +
88V GLU* 1.3 62.7 + - - +
90V CYS* 3.2 2.5 + - - +
91V LYS* 2.9 51.6 + - + +
99V ILE* 3.8 29.2 - - + -
101V ILE* 4.5 9.4 - - + -
117V ALA* 4.1 25.6 - - + +
118V TYR* 4.7 2.2 - - + -
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Residues in contact with GLU 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84V LEU 3.1 13.9 + - - +
85V ASN* 3.2 12.3 + - - +
87V LEU* 1.3 85.1 - - - +
89V GLU* 1.3 61.6 + - - +
91V LYS* 3.0 38.5 + - - +
92V LYS* 3.1 36.5 + - - +
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Residues in contact with GLU 89 (chain V).
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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1S MME 5.2 0.9 - - - +
70V TRP* 3.8 15.6 - - + -
71V LYS* 2.9 34.8 + - - -
85V ASN 3.0 13.4 + - - +
86V GLU* 3.1 13.3 + - - +
88V GLU* 1.3 74.6 - - - +
90V CYS* 1.3 64.5 + - - +
92V LYS* 3.4 14.7 + - + +
93V GLU* 3.3 20.1 + - - +
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Residues in contact with CYS 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V LEU* 4.4 6.1 - - + -
44V PHE* 4.2 17.7 - - - -
70V TRP* 3.8 42.6 - - + -
86V GLU 2.8 16.6 + - - +
87V LEU 3.6 4.9 - - - +
89V GLU* 1.3 75.5 - - - +
91V LYS* 1.3 58.1 + - - +
93V GLU* 3.3 2.6 + - - +
94V TYR* 2.8 32.0 + - - +
99V ILE* 3.7 30.7 - - + -
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Residues in contact with LYS 91 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87V LEU* 2.9 33.6 + - + +
88V GLU* 3.0 38.0 + - - +
90V CYS* 1.3 76.4 - - - +
92V LYS* 1.3 62.2 + - + +
94V TYR 4.3 2.5 - - - -
95V PRO* 3.1 28.3 - - - +
99V ILE* 3.6 22.0 - - + +
117V ALA 5.7 1.0 + - - +
118V TYR* 3.6 37.7 - - + -
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Residues in contact with LYS 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88V GLU* 3.1 26.8 + - - +
89V GLU* 3.5 16.2 - - + +
90V CYS 3.2 0.2 - - - -
91V LYS* 1.3 78.2 - - + +
93V GLU* 1.3 60.0 + - - +
95V PRO* 3.6 9.2 - - - +
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Residues in contact with GLU 93 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3S VAL* 4.2 19.3 + - - +
5S PRO* 5.6 2.9 - - - +
7S GLN* 5.0 1.7 - - - +
70V TRP* 3.1 29.2 - - + -
89V GLU* 3.3 11.9 + - - +
90V CYS 3.3 1.9 + - - +
92V LYS* 1.3 80.0 - - - +
94V TYR* 1.3 88.7 + - + +
95V PRO* 3.5 6.0 - - - +
96V ASN* 4.8 0.7 - - - +
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Residues in contact with TYR 94 (chain V).
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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3S VAL* 4.9 3.1 + - + +
4S TRP 4.3 2.1 + - - -
5S PRO* 3.5 28.4 - - - +
6S THR* 3.8 12.7 + - - -
7S GLN* 3.5 26.2 - - + -
44V PHE* 3.5 42.1 - + + -
46V THR* 4.1 11.9 - - + -
70V TRP* 4.2 15.0 - + - -
90V CYS* 2.8 20.1 + - - +
91V LYS* 3.4 6.6 - - - +
93V GLU* 1.3 109.3 + - + +
95V PRO* 1.3 61.7 - - - +
96V ASN* 3.0 9.7 + - - -
97V ALA* 3.2 25.0 + - + +
99V ILE* 4.4 2.3 - - - +
118V TYR* 4.2 4.5 - - - -
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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