Contacts of the strand formed by residues 149 - 156 (chain A) in PDB entry 2GRU
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 GLY 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ASN* 3.5 1.2 - - - -
146A LEU 2.9 35.7 + - - +
147A THR 3.3 2.4 + - - -
148A SER* 1.3 81.5 - - - +
150A LYS* 1.3 71.7 + - - +
152A LEU* 3.4 15.8 - - - +
321A ASN* 4.7 4.5 - - - -
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Residues in contact with LYS 150 (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* 4.1 24.4 + - + +
73A GLU* 5.2 2.4 - - - +
145A ASN* 3.3 33.4 - - - +
146A LEU 4.4 5.6 + - - -
147A THR 5.4 3.5 + - - -
149A GLY* 1.3 80.2 - - - +
151A ASN* 1.3 72.7 + - + +
152A LEU* 3.2 6.6 + - - +
250A HIS* 5.0 6.5 - - + +
254A LEU* 4.6 21.8 - - + -
321A ASN* 5.4 1.0 + - - -
322A LYS* 3.5 38.5 - - - +
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Residues in contact with ASN 151 (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 LYS* 2.8 31.7 + - - +
108A ASN* 4.7 3.6 + - - +
143A ALA* 3.7 24.2 - - + +
144A VAL 3.2 8.8 + - - -
145A ASN* 2.9 13.0 + - - +
149A GLY 3.7 0.4 + - - -
150A LYS* 1.3 74.7 - - - +
152A LEU* 1.3 63.6 + - - +
153A VAL 3.4 3.6 + - - -
322A LYS* 4.2 17.1 - - + +
603A NAD 3.3 24.0 + - - -
608A PO4 2.9 30.2 + - - +
118B PHE* 5.5 2.1 - - - -
119B ARG* 4.2 13.5 + - - +
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Residues in contact with LEU 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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144A VAL 3.3 2.6 + - - -
146A LEU* 4.1 26.9 - - + +
148A SER* 3.6 12.8 - - - +
149A GLY* 3.4 40.1 + - - +
150A LYS 3.2 6.0 - - - +
151A ASN* 1.3 78.2 - - - +
153A VAL* 1.3 63.4 + - - +
154A GLY 4.2 0.2 - - - -
321A ASN* 4.0 27.4 - - - +
322A LYS* 4.7 1.6 - - - -
88B ILE* 4.6 13.0 - - + -
116B MET 3.4 0.3 - - - +
117B MET* 3.6 1.7 - - - +
118B PHE* 2.8 60.9 + - + +
119B ARG 5.1 0.2 - - - -
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Residues in contact with VAL 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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77A LEU* 4.7 10.5 - - + -
112A VAL* 4.9 0.7 - - - +
143A ALA* 3.4 3.7 - - - -
144A VAL* 2.9 59.4 + - + +
145A ASN 4.4 1.6 - - - +
146A LEU* 4.0 29.4 - - + -
151A ASN 3.4 0.4 - - - -
152A LEU* 1.3 83.8 - - - +
154A GLY* 1.3 59.0 + - - +
84B GLN* 3.5 35.0 - - + +
116B MET* 3.1 18.8 - - + +
117B MET* 4.5 2.9 - - + -
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Residues in contact with GLY 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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112A VAL* 4.8 3.4 - - - -
142A GLN 3.3 12.3 - - - -
143A ALA* 4.0 1.1 - - - -
152A LEU 4.2 0.2 - - - -
153A VAL* 1.3 75.6 - - - +
155A PHE* 1.3 70.2 + - - +
115B GLY 3.5 0.3 - - - +
116B MET* 2.8 42.3 + - - +
119B ARG* 3.3 14.8 - - - +
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Residues in contact with PHE 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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111A GLY 3.9 9.6 - - - -
112A VAL* 3.8 18.8 - - + -
115A GLY* 4.0 10.1 - - - -
116A MET* 3.6 32.8 - - + -
141A LYS* 3.7 0.5 - - - -
142A GLN* 2.8 42.4 + - + +
154A GLY* 1.3 78.6 - - - +
156A TYR* 1.3 67.8 + - + +
157A TYR* 3.8 28.0 - + + -
115B GLY 4.6 6.5 - - - +
116B MET* 4.0 14.4 - - + -
119B ARG* 3.6 18.9 - - - +
155B PHE* 4.0 25.8 - + + -
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Residues in contact with TYR 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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140A ILE* 3.2 17.9 - - + +
141A LYS* 3.7 35.5 + - + +
155A PHE* 1.3 82.9 - - + +
157A TYR* 1.3 66.4 + - - +
158A PRO* 4.3 3.6 - - - +
233A ILE 4.2 8.1 - - - -
234A TYR* 3.5 61.7 + + + -
236A LYS* 3.4 24.3 + - - -
118B PHE 5.3 0.3 + - - -
119B ARG* 3.8 39.4 + - + +
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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