Contacts of the strand formed by residues 153 - 160 (chain A) in PDB entry 2GPC
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 LEU 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A VAL* 4.2 20.2 - - + -
129A LYS 3.6 3.1 - - - -
130A ASP* 3.8 22.9 - - + +
137A LYS* 5.2 5.4 - - + +
139A TYR* 3.7 44.9 - - + -
147A PRO* 3.7 16.9 - - + +
148A LEU* 5.4 0.7 - - - +
150A GLU* 2.9 36.2 + - + +
151A PRO 3.3 2.4 - - - -
152A ASN* 1.3 97.7 - - - +
154A LYS* 1.3 64.0 + - - +
155A PRO* 3.3 8.5 - - - +
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Residues in contact with LYS 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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128A VAL* 3.2 3.2 - - - -
129A LYS* 2.9 48.2 + - + +
131A THR* 4.3 20.4 - - + -
151A PRO 5.0 1.0 + - - -
152A ASN 3.4 2.4 + - - -
153A LEU* 1.3 70.4 - - - +
155A PRO* 1.3 78.3 - - + +
156A LEU* 3.9 3.4 - - + +
193A GLN* 3.4 21.2 + - + +
194A LEU* 3.0 32.8 + - - -
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Residues in contact with PRO 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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73A PHE* 4.4 9.6 - - + -
77A PHE* 3.4 24.1 - - + -
126A TRP* 3.8 29.2 - - + -
127A LEU 4.1 4.3 - - - +
128A VAL* 4.2 4.9 - - + -
147A PRO* 4.5 6.5 - - + -
148A LEU* 4.3 25.1 - - + -
153A LEU 3.3 7.8 - - - +
154A LYS* 1.3 90.6 - - + +
156A LEU* 1.3 60.5 + - - +
193A GLN* 3.4 16.5 - - - +
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Residues in contact with LEU 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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77A PHE* 3.5 11.7 - - - -
81A SER* 4.7 0.5 + - - -
127A LEU* 2.9 37.8 + - + +
129A LYS* 4.0 14.8 - - + +
136A LEU* 4.0 18.2 - - + -
154A LYS* 3.9 12.1 - - + +
155A PRO* 1.3 77.7 - - - +
157A LEU* 1.3 63.3 + - - +
189A ASN* 4.5 2.8 - - - +
190A VAL* 3.5 36.5 + - + +
193A GLN* 3.6 39.8 - - + +
194A LEU* 4.0 25.6 - - + +
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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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77A PHE* 3.4 9.4 - - - -
81A SER* 3.6 29.4 - - - +
108A PHE* 4.7 7.0 - - + -
112A PHE* 4.4 13.7 - - + -
126A TRP* 3.3 9.1 - - - -
127A LEU* 3.0 37.9 + - + -
156A LEU* 1.3 78.8 - - - +
158A THR* 1.3 63.5 + - - +
181A PHE* 4.0 22.4 - - + -
182A TRP* 4.9 2.2 - - + -
185A VAL* 3.7 34.5 - - + -
186A ASN 4.8 0.2 - - - +
187A TRP* 4.7 12.6 - - + -
190A VAL* 3.8 15.0 - - + -
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Residues in contact with THR 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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74A ASN 3.9 7.2 - - - +
77A PHE* 3.8 9.8 - - + -
78A TYR* 3.6 39.0 - - + +
81A SER* 3.3 13.3 + - - -
112A PHE* 4.8 0.4 - - - -
124A TRP* 3.4 19.8 - - + +
125A ALA 3.1 12.5 + - - -
126A TRP* 3.5 28.2 - - + -
157A LEU* 1.3 76.5 - - - +
159A CYS* 1.3 66.4 + - - +
181A PHE* 3.3 19.5 - - - -
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Residues in contact with CYS 159 (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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78A TYR* 4.0 1.3 - - - -
112A PHE* 3.9 15.0 - - + -
116A ALA* 5.2 0.7 - - - -
124A TRP* 3.7 0.3 - - - -
125A ALA* 3.0 29.9 + - + -
158A THR* 1.3 77.5 + - - +
160A ASP* 1.3 65.0 + - - +
161A VAL* 3.4 11.0 + - - +
177A TYR* 3.6 32.8 - - - -
178A VAL* 4.7 7.6 - - - -
181A PHE* 3.7 41.7 - - + -
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Residues in contact with ASP 160 (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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27A HIS* 2.8 10.0 + - - -
75A HIS* 3.4 1.6 + - - -
78A TYR* 3.5 22.1 - - + -
123A GLY 3.6 0.5 - - - +
124A TRP* 3.4 29.1 - - + -
159A CYS* 1.3 69.3 - - - +
161A VAL* 1.3 57.5 + - - +
162A TRP* 3.0 36.3 + - - -
164A HIS* 3.5 0.7 + - - -
165A ALA* 3.7 15.5 - - + +
177A TYR* 2.6 32.1 + - - -
195A FE2 2.0 32.9 - - - -
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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