Contacts of the strand formed by residues 167 - 173 (chain C) in PDB entry 4CYM
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 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C VAL* 3.8 30.5 - - + -
117C VAL* 4.3 15.7 - - + -
118C LEU* 5.7 0.7 - - + -
121C LYS* 3.6 27.8 - - + -
138C ALA* 3.5 15.9 - - + -
140C LEU* 3.8 30.5 - - + -
161C PHE* 4.0 20.4 - + - -
162C CYS* 2.9 39.8 + - + +
163C LYS* 5.0 1.4 - - - +
165C HIS* 3.4 24.7 - - + -
166C GLY* 1.3 78.5 - - - +
168C ALA* 1.3 63.8 + - - +
169C GLY 3.2 8.3 + - - +
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Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 3.5 27.3 - - - +
137C PRO* 5.1 2.2 - - + -
138C ALA 2.9 21.0 + - - +
139C VAL* 4.7 2.2 - - + -
166C GLY 3.8 2.6 + - - -
167C PHE* 1.3 70.7 - - - +
169C GLY* 1.3 56.3 + - - +
187C PHE* 3.2 28.5 - - + -
191C LYS* 3.6 32.8 - - + -
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Residues in contact with GLY 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ALA 4.0 2.4 + - - -
139C VAL* 4.3 4.0 - - - +
140C LEU* 3.3 17.1 + - - +
162C CYS* 3.5 12.9 - - - -
167C PHE* 3.1 5.4 + - - +
168C ALA* 1.3 80.3 - - - +
170C TRP* 1.3 69.8 + - - +
171C PHE* 5.1 0.4 - - - -
187C PHE* 4.0 15.6 - - - -
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Residues in contact with TRP 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C PHE* 6.1 0.2 - + - -
140C LEU* 3.2 23.3 - - + +
142C ALA* 4.5 13.7 - - + -
149C LYS* 5.9 2.0 - - - -
155C PRO* 3.7 42.4 - - + -
158C VAL* 3.2 30.9 - - + +
159C ASP* 2.8 28.4 + - - -
162C CYS* 3.7 24.2 - - + -
169C GLY* 1.3 75.7 - - - +
171C PHE* 1.3 97.4 + - - +
172C GLU* 3.7 34.5 - - + -
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Residues in contact with PHE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C VAL* 3.9 18.6 - - + -
140C LEU 3.2 4.2 + - - -
141C LEU* 3.7 5.8 - - + -
142C ALA 2.9 23.9 + - - -
169C GLY* 5.1 0.2 - - - -
170C TRP* 1.3 110.2 - - - +
172C GLU* 1.3 64.1 + - - +
173C THR* 3.4 17.9 + - + +
180C ASN* 4.1 19.1 - - + +
183C GLU* 3.9 10.8 - - + -
184C ALA* 3.6 36.3 - - + -
187C PHE* 3.5 37.7 - + + -
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Residues in contact with GLU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 3.5 24.0 - - + +
142C ALA* 3.4 7.0 - - - +
145C CYS* 3.9 20.7 - - + +
149C LYS* 3.6 19.4 + - - -
155C PRO* 5.4 5.2 - - - +
170C TRP* 3.7 24.9 - - + -
171C PHE* 1.3 69.7 - - - +
173C THR* 1.3 58.8 + - - +
179C ILE* 3.7 3.7 - - + +
180C ASN* 2.9 34.2 + - - +
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Residues in contact with THR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ILE* 4.5 2.5 - - - +
141C LEU* 3.9 31.0 - - + +
142C ALA 2.8 8.8 + - - +
143C ASN* 2.7 34.1 + - - +
144C LYS 3.0 22.3 + - - -
145C CYS* 3.1 12.4 + - - -
171C PHE* 3.8 15.7 - - + +
172C GLU* 1.3 78.6 - - - +
174C SER* 1.3 60.8 + - - +
179C ILE 3.2 13.5 - - - +
180C ASN 4.2 10.1 - - - +
181C ILE* 4.3 10.5 - - + -
184C ALA* 5.0 0.2 - - + -
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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