Contacts of the strand formed by residues 120 - 127 (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 PRO 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.2 9.4 - - + -
70A LEU* 3.7 39.9 - - + -
71A ILE 3.1 12.6 - - - +
72A SER* 4.4 0.4 - - - -
113A TRP* 4.7 1.1 - - + -
117A PHE* 3.9 10.5 - - + -
118A GLY 3.6 3.4 - - - +
119A ILE* 1.3 85.5 - - + +
121A GLY* 1.3 60.1 + - - +
122A ALA 3.6 3.6 - - - +
140A LEU* 4.1 13.2 - - + -
143A ILE* 4.5 7.9 - - + -
149A ILE* 3.4 45.6 - - + +
151A PHE* 4.0 1.8 - - + -
171A VAL* 4.5 0.9 - - - +
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Residues in contact with GLY 121 (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 2.8 8.6 + - - -
73A ALA* 3.9 17.3 - - - +
119A ILE 3.6 3.6 + - - -
120A PRO* 1.3 73.7 - - - +
122A ALA* 1.3 62.9 + - - +
151A PHE* 3.8 3.1 - - - -
170A PHE* 3.8 8.7 - - - -
171A VAL* 3.1 38.8 + - - +
184A LEU* 4.0 8.8 - - - +
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Residues in contact with ALA 122 (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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70A LEU* 3.6 5.9 - - - +
71A ILE* 2.8 40.6 + - + +
120A PRO* 3.6 2.0 - - - +
121A GLY* 1.3 80.1 + - - +
123A PHE* 1.3 59.7 + - - +
151A PHE* 3.6 10.2 - - - -
168A ILE* 3.8 18.6 - - + -
169A PHE 3.1 16.2 - - - +
170A PHE* 4.0 12.3 - - + -
184A LEU* 4.4 4.0 - - + -
187A TYR* 5.8 0.4 - - + -
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Residues in contact with PHE 123 (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* 3.6 30.7 - - + -
69A GLN 3.1 15.0 - - - +
70A LEU* 4.1 7.6 - - + +
71A ILE* 4.3 4.3 - - - +
122A ALA* 1.3 76.1 - - - +
124A TYR* 1.3 70.0 + - - +
125A ILE* 3.9 15.3 - - + -
135A LEU* 4.0 5.2 - - + -
138A VAL* 3.8 18.2 - - + -
140A LEU* 6.4 0.2 - - + -
151A PHE* 3.8 33.7 - + - -
153A CYS* 3.6 18.6 - - - -
168A ILE* 3.3 6.4 - - - +
169A PHE* 3.0 71.7 + + + -
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Residues in contact with TYR 124 (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* 3.2 7.6 - - - +
69A GLN* 2.9 58.4 + - + +
71A ILE* 3.7 18.1 - - + +
84A VAL* 3.8 21.9 - - + +
123A PHE* 1.3 72.7 - - - +
125A ILE* 1.3 61.2 + - - +
126A LYS* 5.5 1.6 - - + +
166A ASN* 3.6 30.3 - - + +
167A ARG 3.1 19.5 - - - +
168A ILE* 3.5 26.5 - - + +
187A TYR* 3.1 23.9 - - - -
190A GLU* 4.8 6.9 + - - -
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Residues in contact with ILE 125 (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* 5.3 1.3 - - + -
66A ILE* 3.6 24.9 - - + -
67A SER 3.5 10.5 - - - +
68A MET* 3.8 17.0 - - + -
123A PHE* 3.9 9.2 - - + -
124A TYR* 1.3 75.5 - - - +
126A LYS* 1.3 69.8 + - - +
127A ASN 4.2 0.2 - - - -
133A PHE* 4.5 3.1 - - + -
135A LEU* 3.8 31.0 - - + -
157A VAL* 4.0 15.8 - - + +
160A PHE* 5.6 1.4 - - - -
166A ASN* 4.7 1.6 - - - +
167A ARG* 3.4 31.8 + - + +
169A PHE* 3.7 32.3 - - + -
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Residues in contact with LYS 126 (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* 3.3 5.2 - - - +
67A SER* 2.8 45.0 + - - +
69A GLN* 5.8 2.5 - - - +
87A GLU* 3.5 29.5 + - - +
124A TYR* 5.5 1.6 - - + +
125A ILE* 1.3 78.3 - - - +
127A ASN* 1.3 60.9 + - - +
128A PHE* 3.7 23.3 - - + -
157A VAL* 5.4 0.2 - - - -
160A PHE* 4.6 25.0 - - + +
166A ASN* 3.4 39.6 - - - +
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Residues in contact with ASN 127 (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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65A ASN 3.4 4.7 - - - -
66A ILE* 3.6 5.1 - - - +
125A ILE 4.2 0.4 - - - -
126A LYS* 1.3 75.2 - - - +
128A PHE* 1.3 61.3 + - - +
129A MET* 3.1 48.4 - - - +
131A ASP 3.7 5.8 + - - +
133A PHE* 3.2 31.4 - - + -
157A VAL* 3.2 9.4 - - + +
158A TYR* 3.1 14.9 + - - +
159A ASN* 2.9 30.1 + - - -
160A PHE* 3.1 24.1 + - - +
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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