Contacts of the strand formed by residues 127 - 133 (chain A) in PDB entry 2CUY
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.9 5.5 - - - +
123A PRO 4.2 0.4 + - - -
125A GLY 3.3 0.9 - - - -
126A GLU* 1.3 82.3 - - - +
128A ALA* 1.3 64.7 + - - +
165A GLY 3.3 10.3 - - - -
167A ARG* 3.8 4.1 - - - +
190A SER 3.7 18.8 + - - +
192A PRO* 4.1 12.1 - - - -
188B PRO* 3.4 22.7 - - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY* 1.3 77.6 - - - +
129A MET* 1.3 63.9 + - - +
164A SER* 3.2 4.5 - - - -
165A GLY 3.1 30.9 + - - +
167A ARG* 3.9 23.6 - - + -
170A VAL* 3.5 13.3 - - + +
186A PHE* 4.4 14.8 - - + -
189A VAL 4.5 3.8 - - - -
190A SER 5.2 0.2 - - - -
192A PRO* 4.0 5.1 - - - +
188B PRO* 4.2 15.3 - - + -
189B VAL* 4.6 0.9 - - + -
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Residues in contact with MET 129 (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 ALA* 1.3 74.9 - - - +
130A ALA* 1.3 63.8 + - - +
153A ALA* 3.7 20.2 - - + -
154A ASN* 4.8 7.9 - - - +
162A VAL* 3.9 11.7 - - + -
163A ILE 3.2 6.1 - - - +
164A SER* 3.2 14.1 - - - +
170A VAL* 4.6 1.1 - - - -
186A PHE* 3.5 8.6 - - - +
187A LEU* 2.9 39.9 + - + +
189A VAL* 3.7 25.7 + - + +
191A ALA 3.6 12.1 - - - +
192A PRO* 3.9 1.1 - - + -
193A PHE* 3.3 50.5 - - + +
194A HIS* 5.5 0.2 - - + -
188B PRO* 5.6 0.2 - - - +
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Residues in contact with ALA 130 (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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129A MET* 1.3 77.7 - - - +
131A ALA* 1.3 60.5 + - - +
132A VAL* 4.8 0.2 - - - -
161A THR 3.9 0.2 - - - +
162A VAL* 3.3 6.8 - - - +
163A ILE* 2.8 41.7 + - + +
170A VAL* 4.0 13.4 - - + +
174A ALA* 5.7 0.2 - - + -
184A VAL* 4.2 14.6 - - + -
185A VAL 3.4 13.5 - - - +
186A PHE* 3.8 20.6 - - + -
187A LEU* 4.2 1.8 - - - +
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Residues in contact with ALA 131 (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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130A ALA* 1.3 72.7 - - - +
132A VAL* 1.3 61.8 + - - +
133A LEU* 4.1 8.4 - - + +
160A GLN* 6.1 0.7 - - + -
161A THR 3.5 5.2 - - - +
162A VAL* 4.3 10.5 - - + +
183A ARG 3.4 2.4 - - - +
184A VAL* 3.3 5.2 - - - -
185A VAL* 2.8 37.7 + - - +
187A LEU* 4.1 5.5 - - + +
51B GLU* 3.2 45.1 - - + +
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Residues in contact with VAL 132 (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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130A ALA 4.2 7.4 - - - +
131A ALA* 1.3 76.5 - - - +
133A LEU* 1.4 63.2 + - - +
135A LEU* 4.3 3.3 - - + +
140A ILE* 3.8 28.7 - - + +
159A GLU 3.8 1.6 - - - +
160A GLN* 3.6 2.3 + - - -
161A THR* 2.6 40.3 + - - +
163A ILE* 4.3 17.3 - - + -
177A LEU* 3.5 33.7 - - + -
182A ALA* 4.0 21.5 - - + -
183A ARG 3.6 2.5 - - - -
184A VAL* 4.5 6.7 - - + +
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Residues in contact with LEU 133 (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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131A ALA* 4.5 12.3 - - + +
132A VAL* 1.4 83.0 - - - +
134A LYS* 1.3 79.9 + - + +
135A LEU 3.2 3.5 + - - -
159A GLU 3.4 5.4 - - - +
160A GLN* 3.5 34.1 - - + -
182A ALA* 3.5 4.9 - - - +
183A ARG* 2.8 52.3 + - + +
185A VAL* 5.0 3.1 - - + -
49B PRO* 3.9 24.7 - - + -
51B GLU* 4.5 9.2 - - + +
52B ALA* 4.2 20.4 - - + +
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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