Contacts of the strand formed by residues 115 - 123 (chain A) in PDB entry 2IWR
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 GLN 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A SER* 4.6 6.9 + - - -
69A PRO* 3.9 24.8 - - - +
111A LEU* 3.9 2.9 - - - -
112A VAL 2.8 34.3 + - - +
113A ASP 3.3 2.4 - - - +
114A GLY* 1.3 80.3 - - - +
116A THR* 1.3 65.7 + - - +
117A HIS* 3.0 27.5 + - + -
231A VAL* 6.0 0.7 - - - +
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Residues in contact with THR 116 (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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67A SER 5.1 0.3 - - - +
68A ILE* 3.8 26.4 - - + +
69A PRO* 3.5 20.4 - - - +
109A GLU* 4.1 23.8 - - + +
110A MET 3.4 8.7 - - - +
111A LEU* 3.7 15.6 - - - +
115A GLN* 1.3 77.6 - - - +
117A HIS* 1.3 70.4 + - - +
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Residues in contact with HIS 117 (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 ILE* 3.7 5.4 - - - -
69A PRO* 3.3 36.5 - - + +
71A LEU* 3.9 36.6 - - + -
109A GLU* 3.3 4.7 - - - -
110A MET* 2.8 35.8 + - - +
112A VAL* 3.7 21.1 - - + +
115A GLN* 3.0 52.1 + - + -
116A THR* 1.3 73.6 - - - +
118A LEU* 1.3 60.7 + - - +
119A VAL* 3.7 2.6 + - + -
231A VAL* 3.6 21.4 - - + +
234A ARG* 5.6 0.4 - - - -
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Residues in contact with LEU 118 (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 ILE* 3.5 14.4 - - + +
69A PRO 2.8 12.6 + - - +
70A GLU* 3.2 31.4 - - + +
71A LEU 2.9 24.3 + - - +
107A LYS* 4.0 24.0 - - + -
108A LYS* 3.9 5.6 - - - +
109A GLU* 3.9 22.7 - - + +
117A HIS* 1.3 70.9 - - - +
119A VAL* 1.3 62.9 + - - +
120A LEU* 3.8 18.2 + - + +
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Residues in contact with VAL 119 (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 LEU* 3.5 25.1 - - + +
73A LEU* 3.8 29.4 - - + -
90A PHE* 5.4 1.6 - - + -
107A LYS* 3.2 4.2 - - - -
108A LYS* 2.9 40.4 + - + +
110A MET* 3.5 45.8 - - + -
117A HIS* 4.6 2.0 - - + +
118A LEU* 1.3 73.2 - - - +
120A LEU* 1.3 64.3 + - - +
121A ILE* 3.9 19.5 + - + +
227A ALA* 4.4 1.8 - - + -
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Residues in contact with LEU 120 (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 GLU* 4.2 24.0 - - + +
71A LEU 2.9 12.8 + - - +
72A ARG* 3.8 20.6 - - + -
73A LEU* 2.8 29.0 + - - +
105A GLN* 4.6 13.9 - - - +
106A TYR 3.5 5.2 - - - +
107A LYS* 3.7 24.0 - - + -
118A LEU* 4.1 22.0 - - + +
119A VAL* 1.3 76.2 - - - +
121A ILE* 1.3 62.4 + - - +
135A TRP* 4.0 19.3 - - + +
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Residues in contact with ILE 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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73A LEU* 3.2 13.5 - - + +
75A VAL* 4.1 18.2 - - + -
87A ILE* 4.0 25.6 - - + -
90A PHE* 3.8 22.9 - - + -
91A LEU* 4.4 14.4 - - + -
105A GLN* 3.6 3.6 - - - +
106A TYR* 2.9 43.3 + - + +
108A LYS* 5.6 0.7 - - + -
119A VAL* 3.9 18.4 - - + +
120A LEU* 1.3 79.2 - - - +
122A ARG* 1.3 65.6 + - - +
135A TRP* 4.6 0.4 - - - -
223A PHE* 3.7 28.0 - - + -
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Residues in contact with ARG 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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73A LEU 3.1 7.1 + - - -
74A GLY* 3.3 5.4 - - - -
75A VAL* 2.9 24.2 + - - -
104A GLU 4.2 8.7 - - - +
105A GLN* 3.9 18.6 - - + +
106A TYR* 6.0 0.4 - - - -
121A ILE* 1.3 78.0 - - - +
123A GLU* 1.3 63.8 + - - +
124A GLU* 5.8 1.1 - - - +
132A PHE* 3.7 8.8 - - + -
135A TRP* 4.1 17.9 - - + -
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Residues in contact with GLU 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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75A VAL* 3.2 13.9 - - + +
83A LYS* 3.6 20.1 + - - +
84A SER* 2.6 32.3 + - - -
87A ILE* 3.7 18.5 - - + +
99A GLU 4.8 0.2 - - - +
100A LYS* 3.4 10.0 - - - +
101A THR* 2.8 41.7 + - - +
104A GLU 4.5 8.7 + - - +
122A ARG* 1.3 78.5 - - - +
124A GLU* 1.3 73.5 + - - +
125A ALA* 4.2 5.1 + - - +
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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