Contacts of the strand formed by residues 151 - 158 (chain A) in PDB entry 1IMG
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 VAL 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A MET* 3.3 43.6 - - + +
145A GLY* 3.3 8.8 - - - +
148A ASN* 3.1 26.0 + - - +
149A PRO 4.6 0.2 - - - -
150A ASN* 1.4 86.0 - - - +
152A LYS* 1.3 60.7 + - - +
153A GLU 3.7 0.7 - - - +
154A ILE* 4.6 10.5 - - + -
169A GLU* 3.9 37.0 - - + +
170A LEU 4.1 3.6 - - - -
171A ALA* 4.8 4.7 - - + +
188A ARG* 5.9 1.8 - - - +
220A HIS* 6.1 2.5 - - - +
267A PHE* 6.3 0.9 - - + -
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Residues in contact with LYS 152 (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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145A GLY* 3.1 24.6 - - - +
148A ASN 4.8 1.1 - - - -
149A PRO 5.0 2.2 - - - +
150A ASN 3.6 2.2 + - - -
151A VAL* 1.3 73.2 - - - +
153A GLU* 1.4 72.0 + - + +
170A LEU* 3.3 37.3 + - - +
171A ALA 3.9 6.5 + - - -
172A ALA* 4.1 25.9 - - + +
173A GLU* 4.7 4.9 + - - +
181A PRO* 3.7 28.1 - - - +
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Residues in contact with GLU 153 (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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145A GLY* 4.6 1.6 - - - -
151A VAL 3.7 0.4 - - - -
152A LYS* 1.4 88.7 - - + +
154A ILE* 1.3 55.2 + - - +
155A LYS* 4.0 12.3 - - + +
168A HIS* 2.8 34.2 + - + +
169A GLU* 4.4 0.4 - - - -
170A LEU* 3.2 45.3 + - + +
209A MET* 6.0 0.3 - - - +
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Residues in contact with ILE 154 (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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141A MET* 3.4 32.3 - - + +
142A GLU* 3.6 24.6 + - - +
144A MET* 4.1 10.5 - - + -
145A GLY* 3.5 28.9 - - - +
151A VAL* 4.6 11.7 - - + -
152A LYS 4.3 0.2 - - - -
153A GLU* 1.3 70.8 - - - +
155A LYS* 1.3 61.8 + - - +
167A THR* 4.0 21.1 - - + +
168A HIS 3.5 2.9 - - - -
169A GLU* 3.9 21.8 - - + -
188A ARG* 3.7 28.9 - - - +
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Residues in contact with LYS 155 (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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142A GLU* 3.8 8.7 - - - +
153A GLU* 4.8 13.7 - - + +
154A ILE* 1.3 75.1 - - - +
156A VAL* 1.3 66.8 + - - +
157A LEU* 3.6 14.0 + - + +
167A THR* 3.5 3.2 - - - -
168A HIS* 3.0 57.2 + - + +
209A MET* 4.2 15.5 - - + +
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Residues in contact with VAL 156 (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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141A MET* 3.8 28.7 - - + -
142A GLU* 3.5 30.9 + - + +
155A LYS* 1.3 76.0 - - - +
157A LEU* 1.3 64.3 + - - +
158A GLN 5.1 0.4 - - - +
159A LYS* 4.0 30.7 - - + +
165A PHE* 5.3 2.7 - - + -
166A ILE 3.7 6.5 - - - +
167A THR* 3.9 15.5 - - + -
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Residues in contact with LEU 157 (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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155A LYS* 4.3 18.4 - - - +
156A VAL* 1.3 78.5 - - - +
158A GLN* 1.4 60.9 + - - +
166A ILE* 3.1 13.3 + - + -
168A HIS* 4.1 19.7 - - + +
185A VAL* 3.8 25.6 - - + -
206A PHE* 3.7 37.2 - - + -
208A ASN* 5.2 6.7 - - + -
209A MET* 3.8 33.4 - - + -
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Residues in contact with GLN 158 (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 GLU* 3.9 27.8 + - - +
75A TYR* 3.7 26.6 - - - -
156A VAL* 5.6 0.2 - - - -
157A LEU* 1.4 79.3 - - - +
159A LYS* 1.3 69.6 + - - +
160A ILE* 3.3 17.8 + - + +
166A ILE* 3.2 34.9 + - + +
206A PHE* 3.8 29.0 - - + -
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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