Contacts of the strand formed by residues 127 - 133 (chain B) in PDB entry 2GPY
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 PHE 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ARG* 3.4 30.3 - - + +
58B ILE 3.6 19.3 - - - -
59B LEU* 3.5 48.0 - - + -
80B THR 5.8 0.2 - - - -
82B VAL* 3.8 23.6 - - + -
121B LEU* 4.2 13.5 - - + -
124B TYR* 4.1 15.5 - + + -
125B PRO 3.8 11.4 - - - -
126B LEU* 1.3 74.2 - - - +
128B ASP* 1.3 62.6 + - - +
129B VAL 3.4 15.0 - - - +
149B MSE 2.9 28.0 + - + +
150B VAL* 3.4 8.3 - - + -
151B ARG* 2.9 27.1 + - - +
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PRO* 3.6 19.1 - - + -
56B ALA* 2.8 32.1 + - - +
57B ARG* 2.9 23.4 + - - +
126B LEU 5.3 1.8 - - - +
127B PHE* 1.3 72.4 - - - +
129B VAL* 1.3 62.5 + - - +
150B VAL* 4.5 1.1 - - - -
151B ARG* 2.7 43.0 + - - +
154B GLY* 3.3 5.2 - - - -
155B LEU* 2.9 25.7 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.9 12.1 - - + -
55B PRO* 3.6 30.7 - - + -
57B ARG 3.3 2.0 + - - -
58B ILE* 3.5 22.7 - - + -
59B LEU 2.9 25.6 + - - -
72B MSE 5.8 0.4 - - - -
127B PHE* 3.4 8.8 - - - +
128B ASP* 1.3 85.4 - - - +
130B LEU* 1.3 70.4 + - - +
131B PHE* 4.4 2.5 - - + +
150B VAL* 4.7 1.8 - - - -
155B LEU* 3.2 22.4 - - + +
157B LEU* 3.7 26.9 - - + -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.3 38.8 - - + +
61B ILE* 3.9 20.4 - - + -
129B VAL* 1.3 74.3 - - - +
131B PHE* 1.3 61.5 + - - +
132B ILE* 4.0 15.7 - - + -
142B PHE 4.5 3.8 - - - +
143B PHE* 4.9 1.8 - - - +
146B TYR* 3.6 33.4 - - + -
147B SER 4.0 3.1 - - - +
150B VAL* 3.5 18.1 - - + +
155B LEU 2.8 6.9 + - - +
156B ILE* 3.3 26.7 - - + +
157B LEU 2.8 26.7 + - - +
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B MSE 3.9 16.2 - - + -
43B MSE 5.8 0.4 - - + -
46B LEU* 3.7 27.8 - - + -
58B ILE* 4.9 4.5 - - + -
59B LEU 2.8 14.1 + - - +
60B GLU* 3.5 30.3 - - + +
61B ILE* 3.1 27.2 + - - +
68B SER* 3.8 18.4 - - - -
72B MSE 4.0 17.5 - - + -
129B VAL* 4.7 9.4 - - + -
130B LEU* 1.3 73.8 - - - +
132B ILE* 1.3 72.8 + - - +
133B ASP* 6.2 0.4 - - + -
157B LEU* 3.5 23.3 - - + -
158B SER 5.0 0.2 - - - -
159B ASP* 4.0 20.0 - - + -
208B ILE* 6.0 0.9 - - + -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 3.7 33.0 - - + -
130B LEU* 4.0 13.2 - - + -
131B PHE* 1.3 86.2 - - - +
133B ASP* 1.3 59.9 + - - +
134B ALA 4.2 0.2 - - - -
139B TYR* 3.5 31.2 - - + +
142B PHE* 4.3 13.2 - - + -
143B PHE* 4.0 29.6 - - + +
156B ILE* 4.0 20.6 - - + -
157B LEU 2.9 14.2 + - - +
158B SER* 3.2 4.2 - - - +
159B ASP 3.0 21.8 + - - -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 5.5 1.7 - - - +
61B ILE 5.0 2.8 + - - +
131B PHE* 6.2 0.4 - - + -
132B ILE* 1.3 78.2 - - - +
134B ALA* 1.3 59.5 + - - +
135B ALA* 2.7 34.8 + - - +
136B LYS* 3.1 61.7 + - + +
139B TYR* 3.6 10.1 - - - +
142B PHE* 5.9 2.4 - - - -
159B ASP* 3.6 11.2 - - + +
160B ASN* 2.9 30.0 + - - -
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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