Contacts of the strand formed by residues 66 - 76 (chain A) in PDB entry 2IUK
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 ILE 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL* 6.2 1.1 - - + -
17A LEU* 4.8 4.5 - - + -
61A PHE* 3.9 13.5 + - + +
63A GLY 4.3 1.4 + - - -
65A ASN* 1.3 84.4 - - + +
67A SER* 1.3 58.0 + - - +
68A MET* 5.1 0.2 - - + -
89A TYR* 3.4 5.4 - - - +
90A LEU* 3.2 56.1 + - + +
125A ILE* 3.6 37.7 - - + -
126A LYS 3.3 6.3 - - - +
127A ASN* 3.6 8.5 - - - +
129A MET* 4.0 13.7 - - + -
133A PHE* 3.3 37.5 - - + -
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Residues in contact with SER 67 (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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66A ILE* 1.3 74.0 - - - +
68A MET* 1.3 67.7 + - - +
87A GLU* 3.1 36.0 + - - +
88A VAL 3.6 10.3 - - - -
89A TYR* 3.7 23.1 - - - +
125A ILE* 3.5 3.5 - - - +
126A LYS* 2.8 35.1 + - - +
128A PHE* 3.4 11.1 - - - -
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Residues in contact with MET 68 (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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15A VAL* 3.7 28.9 - - - -
67A SER* 1.3 80.8 - - - +
69A GLN* 1.3 61.4 + - - +
70A LEU* 4.5 2.2 - - + -
86A LYS 3.6 0.7 - - - +
87A GLU* 3.7 0.4 - - - -
88A VAL 3.0 29.8 + - - +
90A LEU* 4.9 7.0 - - + -
109A ILE* 4.0 8.7 - - + -
111A PHE* 3.5 35.5 - - + -
123A PHE* 3.6 34.3 - - + -
124A TYR 3.2 10.1 - - - +
125A ILE* 3.8 24.2 - - + -
138A VAL* 4.2 17.0 - - + -
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Residues in contact with GLN 69 (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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68A MET* 1.3 75.4 - - - +
70A LEU* 1.3 66.9 + - - +
71A ILE* 4.5 0.5 - - - +
84A VAL* 4.4 14.1 - - + +
85A GLY 3.8 14.8 - - - +
86A LYS* 4.8 3.6 + - - -
87A GLU* 3.7 42.4 + - + +
123A PHE* 3.1 5.4 - - - +
124A TYR* 2.9 67.9 + - + +
126A LYS* 5.8 1.8 - - - +
166A ASN* 4.3 6.5 + - - +
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Residues in contact with LEU 70 (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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11A ILE* 4.2 9.0 - - + -
68A MET* 4.5 2.5 - - + -
69A GLN* 1.3 74.3 - - - +
71A ILE* 1.3 61.3 + - - +
84A VAL* 3.3 4.5 - - - +
85A GLY 2.9 34.3 + - - +
111A PHE* 3.6 58.7 - - + -
112A GLU 5.8 0.2 - - - +
117A PHE* 3.3 17.9 - - + -
120A PRO* 3.7 30.7 - - + -
122A ALA 3.7 2.7 - - - +
123A PHE* 4.1 17.7 - - + -
140A LEU* 4.0 15.5 - - + -
151A PHE* 5.8 0.7 - - + -
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Residues in contact with ILE 71 (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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69A GLN 4.5 2.0 - - - +
70A LEU* 1.3 79.1 - - - +
72A SER* 1.3 63.1 + - - +
82A GLY 4.2 0.9 - - - +
83A LYS 3.1 9.2 - - - +
84A VAL* 3.8 12.8 - - + -
117A PHE* 3.7 3.4 - - - -
120A PRO* 3.1 4.0 - - - +
121A GLY 2.8 32.1 + - - -
122A ALA* 2.8 22.8 + - + +
123A PHE* 4.4 4.7 - - - -
124A TYR* 3.7 39.9 - - + -
168A ILE* 4.0 18.8 - - + -
184A LEU* 4.5 7.4 - - + -
187A TYR* 3.9 37.2 - - + -
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Residues in contact with SER 72 (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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71A ILE* 1.3 71.5 - - - +
73A ALA* 1.3 57.5 + - - +
74A THR 3.2 4.2 + - - -
75A GLN 2.8 27.5 + - - -
82A GLY* 3.5 6.9 - - - -
83A LYS* 3.0 13.6 + - - -
117A PHE* 2.5 45.7 + - - -
118A GLY* 3.6 4.7 - - - -
119A ILE 3.7 4.3 - - - -
121A GLY 4.5 0.2 - - - -
183A PRO* 3.2 21.8 - - - +
184A LEU* 4.3 4.9 - - - +
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Residues in contact with ALA 73 (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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71A ILE 3.7 2.4 + - - -
72A SER* 1.3 72.8 - - - +
74A THR* 1.3 62.2 + - - +
119A ILE* 2.9 19.1 + - + +
120A PRO 4.7 0.2 - - - -
121A GLY* 3.9 12.7 - - - +
175A TYR* 6.0 1.1 - - - +
181A PRO* 3.8 14.2 - - + +
183A PRO* 3.3 23.6 - - - +
184A LEU* 4.0 23.6 - - + -
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Residues in contact with THR 74 (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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72A SER* 3.2 0.8 + - - -
73A ALA* 1.3 84.3 + - - +
75A GLN* 1.3 82.2 + - - +
76A THR* 5.1 0.7 + - - -
118A GLY* 4.0 11.9 - - - -
119A ILE* 3.9 29.1 + - + +
183A PRO* 4.0 9.0 - - - +
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Residues in contact with GLN 75 (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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72A SER* 2.8 17.5 + - - -
74A THR* 1.3 98.8 + - + +
76A THR* 1.3 68.3 + - - +
82A GLY* 3.3 3.8 - - - -
83A LYS* 2.7 40.5 + - + +
116A SER* 3.1 30.5 - - - +
117A PHE 3.1 18.8 - - - +
118A GLY* 4.3 0.9 - - - +
183A PRO* 4.5 0.4 - - - -
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Residues in contact with THR 76 (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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74A THR 5.3 0.4 - - - -
75A GLN* 1.3 86.2 + - - +
77A ASP* 1.3 83.9 + - - +
80A GLY* 3.3 34.1 + - - -
81A ASN 3.4 6.9 + - - -
83A LYS* 3.3 22.8 + - - -
183A PRO* 3.6 16.4 - - - +
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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