Contacts of the strand formed by residues 160 - 166 (chain B) 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 GLN 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PRO* 3.2 44.3 - - + +
51A GLU* 4.2 13.7 + - - +
132B VAL 3.5 4.3 - - - -
133B LEU* 4.7 10.1 - - + -
155B LEU 4.1 0.2 - - - -
156B ASN* 3.1 19.4 + - + +
157B ALA* 3.0 49.4 + - + +
158B PRO 3.8 0.2 + - - -
159B GLU* 1.3 84.6 - - + +
161B THR* 1.3 61.1 + - - +
276B GLY 4.8 0.2 + - - -
277B LEU* 3.7 18.6 - - - +
280B ARG* 4.0 15.6 - - + +
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Residues in contact with THR 161 (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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131B ALA* 3.7 1.0 - - - +
132B VAL* 2.7 42.0 + - - +
135B LEU 5.2 0.2 + - - -
137B LEU* 4.3 8.7 + - + +
140B ILE* 3.6 27.5 - - + +
152B ILE* 4.0 26.2 - - + -
154B ASN 3.2 15.5 + - - +
155B LEU* 4.3 11.8 - - + +
157B ALA 4.4 3.5 + - - -
158B PRO 4.8 4.0 + - - -
159B GLU 5.1 0.2 - - - -
160B GLN* 1.3 80.5 + - - +
162B VAL* 1.3 72.9 + - - +
163B ILE* 4.6 2.5 - - + -
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Residues in contact with VAL 162 (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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51A GLU* 5.8 2.0 - - - +
129B MET* 3.9 24.0 - - + -
130B ALA 3.5 10.5 - - - +
131B ALA* 4.4 15.3 - - + -
152B ILE* 3.6 3.8 - - - -
153B ALA* 2.6 38.0 + - + -
154B ASN* 3.0 41.3 + - + +
156B ASN* 3.6 18.6 - - - +
160B GLN 5.8 0.2 - - - -
161B THR* 1.3 78.1 - - - +
163B ILE* 1.3 66.3 + - - +
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Residues in contact with ILE 163 (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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129B MET* 3.6 4.0 - - - +
130B ALA* 2.9 51.8 + - + +
132B VAL* 4.3 8.1 - - + -
140B ILE* 4.3 9.4 - - + -
144B LEU* 4.1 10.5 - - + -
150B VAL* 4.4 9.2 - - + -
151B GLU 3.1 10.5 - - - +
152B ILE* 4.0 23.6 - - + -
161B THR* 4.6 3.1 - - + -
162B VAL* 1.3 79.6 - - - +
164B SER* 1.3 65.2 + - - +
170B VAL* 4.5 9.6 - - + +
173B ALA* 4.0 22.0 - - + -
174B ALA* 4.9 1.6 - - - +
177B LEU* 3.9 24.7 - - + -
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Residues in contact with SER 164 (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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128B ALA 3.6 14.1 - - - -
129B MET* 4.4 8.1 - - - -
150B VAL* 3.5 0.9 - - - +
151B GLU* 2.7 40.4 + - - +
153B ALA* 3.2 11.7 - - - +
163B ILE* 1.3 77.3 - - - +
165B GLY* 1.3 57.8 + - - +
170B VAL* 3.8 8.7 - - - -
192B PRO* 4.0 10.1 - - - -
193B PHE 2.9 27.1 + - - -
194B HIS 4.1 0.2 + - - -
195B SER* 3.7 10.3 - - - -
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Residues in contact with GLY 165 (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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127B GLY* 3.4 6.2 - - - -
128B ALA 3.1 23.7 + - - -
149B GLY 2.9 10.1 - - - -
151B GLU* 5.5 1.1 - - - -
164B SER* 1.3 79.2 - - - +
166B ARG* 1.3 69.1 + - - -
170B VAL* 3.4 1.5 - - - +
192B PRO* 3.6 12.8 - - - +
195B SER* 4.5 4.3 - - - -
197B LEU* 3.7 12.8 - - - -
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Residues in contact with ARG 166 (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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126B GLU 3.5 7.9 - - - +
148B GLU* 4.0 19.1 + - - +
149B GLY* 2.5 34.1 + - - +
165B GLY* 1.3 70.3 - - - -
167B ARG* 1.3 67.8 + - - +
168B GLN* 3.7 34.1 + - - +
169B ALA* 3.1 23.0 + - + +
170B VAL* 2.9 23.7 + - - +
197B LEU* 3.7 17.8 - - + +
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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