Contacts of the strand formed by residues 56 - 65 (chain A) in PDB entry 2IUI
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 ASN 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU 3.6 0.5 - - - +
52A ARG* 3.7 6.4 - - - +
53A LYS 3.1 33.0 + - - +
54A GLY* 3.0 17.8 + - - -
55A GLY* 1.3 78.0 - - - +
57A ASN* 1.3 67.2 + - - +
58A LYS* 2.7 32.5 + - - +
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Residues in contact with ASN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 2.8 42.6 + - - +
26A LEU* 3.7 17.4 - - + +
50A THR* 3.8 18.1 - - + +
51A LEU 3.5 4.5 - - - -
52A ARG* 3.1 30.2 + - - +
56A ASN* 1.3 75.0 - - - +
58A LYS* 1.3 62.1 + - - +
59A LEU* 3.2 20.6 - - + +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU 3.5 1.2 - - - +
50A THR* 3.3 6.8 - - - -
51A LEU* 2.8 50.5 + - + +
53A LYS* 3.4 40.1 + - + -
56A ASN* 2.7 28.8 + - - +
57A ASN* 1.3 70.2 - - - +
59A LEU* 1.3 62.3 + - - +
60A ILE* 3.6 5.9 + - + +
98A LYS* 5.1 17.4 - - - +
99A LEU* 4.2 15.3 - - + -
201C SER* 5.2 10.7 - - - +
205C VAL* 3.6 23.8 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 4.4 30.1 - - + +
23A ASN* 6.2 0.2 - - - +
37A ARG* 3.6 27.1 - - - +
48A THR* 3.8 11.2 - - + -
49A LEU 3.7 0.9 - - - -
50A THR* 3.9 15.5 - - + +
57A ASN* 3.2 23.8 - - + +
58A LYS* 1.3 71.7 - - - +
60A ILE* 1.3 59.1 + - - +
203C ASP* 4.3 11.5 + - - +
204C PTR 3.3 27.7 - - + +
205C VAL* 2.7 34.6 + - - +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 3.6 1.8 - - - +
49A LEU* 2.8 64.8 + - + +
51A LEU* 4.0 31.6 - - + -
58A LYS* 4.3 5.8 - - + +
59A LEU* 1.3 77.5 - - - +
61A LYS* 1.3 63.4 + - - +
71A PHE* 3.9 20.6 - - + -
92A LEU* 4.6 5.6 - - + -
99A LEU* 4.3 14.6 - - + -
204C PTR 4.0 2.9 - - - -
205C VAL* 4.3 15.9 - - + +
207C MET* 3.7 33.0 - - + -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.6 17.9 - - - +
41A THR* 4.8 8.3 - - + -
46A ASP* 3.2 27.4 - - - +
47A TYR 3.5 8.4 + - - -
48A THR* 2.5 31.1 + - - -
60A ILE* 1.3 75.5 - - - +
62A ILE* 1.3 59.9 + - - +
63A PHE* 3.6 45.6 + - + -
71A PHE* 3.7 15.9 - - - +
204C PTR 3.2 43.2 + - + +
205C VAL 5.4 2.0 + - - -
207C MET* 5.6 1.7 - - - +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.1 15.7 - - + -
45A GLY 4.9 0.3 - - - +
46A ASP* 2.9 18.9 - - - +
47A TYR* 2.9 31.1 + - + +
49A LEU* 4.0 28.5 - - + +
61A LYS* 1.3 73.7 - - - +
63A PHE* 1.3 68.4 + - - +
64A HIS* 3.9 0.9 + - - +
69A TYR* 4.3 13.0 - - + -
70A GLY 3.9 4.3 - - - +
71A PHE* 3.9 18.8 - - + -
80A VAL* 4.0 25.6 - - + -
83A LEU* 3.6 24.0 - - + -
84A ILE* 4.7 4.7 - - + -
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Residues in contact with PHE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASP* 3.8 5.4 - - - -
61A LYS* 3.8 34.5 - - + -
62A ILE* 1.3 75.2 - - - +
64A HIS* 1.3 58.9 + - - +
65A ARG* 4.1 26.2 - - - -
69A TYR* 3.4 9.7 - - - -
70A GLY 2.9 34.9 + - - +
71A PHE 3.0 31.0 - - - -
72A SER* 4.2 5.8 - - - -
75A LEU* 3.9 17.2 - - + +
207C MET* 6.2 0.4 - - + -
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Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A HIS* 3.2 33.8 - - - +
45A GLY* 3.1 33.0 - - - +
46A ASP* 3.9 2.8 + - - +
63A PHE* 1.3 76.7 - - - +
65A ARG* 1.3 81.1 + - - +
66A ASP 4.2 16.2 - - - -
67A GLY* 4.4 7.6 - - - -
68A LYS 3.2 13.4 + - - -
69A TYR* 3.2 35.2 + + + -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A HIS* 3.2 34.7 + - + +
46A ASP* 3.2 23.6 + - - -
63A PHE* 4.3 21.3 - - - -
64A HIS* 1.3 97.7 + - - +
66A ASP* 1.3 74.2 + - - +
68A LYS* 2.9 30.2 + - - +
75A LEU* 3.4 24.8 - - + +
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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