Contacts of the strand formed by residues 83 - 94 (chain Y) in PDB entry 1IRA
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 83 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2Y LYS* 5.1 0.9 - - - +
4Y LYS* 5.3 4.3 - - + -
29Y ASN 5.5 1.1 - - - -
30Y GLU* 3.8 21.6 + - + +
32Y LYS* 3.4 49.8 - - + +
78Y VAL* 4.0 28.0 - - + -
79Y ARG* 3.2 1.4 - - - +
80Y ASN* 2.6 38.5 + - + +
82Y SER* 1.3 81.1 - - - +
84Y CYS* 1.3 75.9 + - - +
85Y LEU* 3.1 35.6 - - + +
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Residues in contact with CYS 84 (chain Y).
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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2Y LYS 3.2 11.0 + - - +
3Y CYS* 2.0 52.4 - - - -
4Y LYS* 2.8 24.1 + - - +
77Y VAL* 3.5 26.5 - - - -
78Y VAL 3.0 7.9 - - - +
79Y ARG* 4.4 14.4 - - + -
83Y TYR* 1.3 87.1 - - - +
85Y LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y CYS* 4.7 0.7 - - - -
4Y LYS* 3.5 17.7 - - + +
5Y GLU 3.5 22.4 - - - +
6Y ARG* 3.8 14.6 - - + +
26Y LEU* 4.3 2.9 - - + -
30Y GLU* 3.6 28.5 - - + +
76Y CYS 3.6 1.4 - - - +
77Y VAL* 3.1 6.5 - - - +
78Y VAL* 2.8 37.1 + - + +
83Y TYR* 3.1 29.4 - - + +
84Y CYS* 1.3 74.7 - - - +
86Y ARG* 1.3 75.7 + - - +
87Y ILE* 3.5 22.5 - - + +
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Residues in contact with ARG 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Y ASP* 2.9 35.5 + - - +
3Y CYS* 4.1 15.3 - - + +
5Y GLU* 3.2 37.5 + - - +
6Y ARG 2.8 27.4 + - - +
42Y SER* 2.9 33.7 + - - -
75Y TYR* 3.6 29.2 - - + -
76Y CYS 3.5 3.1 - - - -
77Y VAL* 3.8 23.4 - - + +
84Y CYS* 5.2 0.2 - - - -
85Y LEU* 1.3 77.2 - - - +
87Y ILE* 1.3 61.2 + - - +
88Y LYS 4.0 0.2 + - - -
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Residues in contact with ILE 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y ARG* 3.1 32.5 - - + +
8Y GLU* 4.0 12.1 - - + +
24Y CYS* 4.7 0.4 - - - -
25Y PRO* 3.6 27.8 - - + +
26Y LEU* 3.3 31.6 - - + -
74Y TYR 3.6 0.3 - - - +
75Y TYR* 3.2 26.9 - - - +
76Y CYS* 3.0 26.0 + - - +
85Y LEU* 3.5 28.3 - - + -
86Y ARG* 1.3 75.2 - - - +
88Y LYS* 1.3 63.8 + - - +
89Y ILE* 3.7 12.5 + - + +
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Residues in contact with LYS 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y GLU* 5.0 3.8 - - - +
6Y ARG 2.8 14.9 + - - +
7Y GLU* 3.4 34.8 + - + +
8Y GLU* 3.1 22.0 + - - +
73Y HIS* 3.4 45.3 + - + +
74Y TYR 3.6 4.5 - - - -
75Y TYR* 3.6 37.3 + - + +
86Y ARG 4.0 0.4 + - - -
87Y ILE* 1.3 71.3 - - - +
89Y ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y GLU* 4.5 9.4 - - + -
10Y ILE 5.8 0.7 - - - +
22Y ARG* 4.5 18.8 - - + +
23Y PRO 5.3 1.1 - - - +
25Y PRO* 3.7 35.2 - - + -
37Y TRP* 3.3 33.7 - - + -
61Y LEU* 4.7 2.0 - - + -
73Y HIS* 3.1 30.0 + - - +
74Y TYR* 3.0 35.7 + - + +
76Y CYS* 4.9 0.4 - - - -
87Y ILE* 3.7 13.2 + - + +
88Y LYS* 1.3 74.5 - - - +
90Y SER* 1.3 65.6 + - - +
91Y ALA* 5.4 2.5 - - + -
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Residues in contact with SER 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y GLU 5.3 6.6 + - - -
10Y ILE 4.4 6.3 + - - +
11Y ILE* 3.5 48.3 - - - +
12Y LEU 3.8 4.9 + - - -
22Y ARG* 4.0 3.6 + - - -
72Y GLY* 3.6 8.0 + - - -
73Y HIS* 3.6 22.0 + - - -
89Y ILE* 1.3 79.0 - - - +
91Y ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Y ILE* 4.9 1.4 - - - +
22Y ARG* 3.5 23.6 - - + +
63Y PHE* 4.7 2.9 - - + -
71Y SER* 3.2 3.2 - - - -
72Y GLY* 2.8 37.7 + - - +
74Y TYR* 4.0 17.7 - - + -
89Y ILE* 4.3 3.1 - - + -
90Y SER* 1.3 75.9 + - - +
92Y LYS* 1.3 61.1 + - - +
93Y PHE* 3.8 21.5 - - + -
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Residues in contact with LYS 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Y ILE* 4.3 19.1 - - + -
12Y LEU 3.4 7.0 + - - +
13Y VAL* 3.3 25.8 - - + -
14Y SER 2.9 24.9 + - - -
22Y ARG* 4.1 0.5 + - - -
71Y SER* 3.6 11.7 - - - +
90Y SER 4.3 0.2 + - - -
91Y ALA* 1.3 76.2 - - - +
93Y PHE* 1.3 68.4 + - - +
94Y VAL* 3.2 27.8 - - + +
105Y GLN* 3.4 23.4 + - - +
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Residues in contact with PHE 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Y SER* 3.3 21.3 - - - +
15Y SER 4.3 3.4 - - - -
16Y ALA* 4.9 3.4 - - - +
20Y ASP* 3.7 18.4 - - - -
22Y ARG* 4.1 9.6 - - - -
63Y PHE* 3.6 44.2 - + - -
66Y ALA* 3.4 27.6 - - + -
67Y LYS 3.9 17.5 - - - +
68Y VAL* 3.6 23.7 - - - +
70Y ASP* 3.8 12.3 - - + -
71Y SER* 2.8 33.9 + - - +
91Y ALA* 3.8 17.5 - - + -
92Y LYS* 1.3 75.8 + - - +
94Y VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y VAL* 3.6 22.2 - - + -
14Y SER 2.8 21.1 + - - +
15Y SER* 3.5 6.1 - - - +
16Y ALA* 2.7 34.9 + - - +
68Y VAL* 4.8 1.3 - - - -
92Y LYS* 3.2 31.2 - - - +
93Y PHE* 1.3 75.0 - - - +
95Y GLU* 1.3 61.9 + - - +
103Y ASN* 3.8 28.0 - - + +
105Y GLN* 3.3 17.0 - - - +
106Y ALA* 4.6 6.1 - - + -
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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