Contacts of the strand formed by residues 168 - 174 (chain C) in PDB entry 5AQP
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 ASN 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C THR* 2.7 19.8 + - + +
141C ASN* 2.8 29.7 + - - +
142C ALA 3.0 24.0 + - - -
166C GLY 4.0 0.6 + - - -
167C LEU* 1.3 70.1 - - - +
169C VAL* 1.4 63.1 + - - +
170C LEU* 3.2 20.0 + - - +
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Residues in contact with VAL 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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142C ALA 3.4 7.4 - - - +
144C VAL* 4.2 16.6 - - + -
158C THR 5.5 0.2 - - - +
159C LYS* 3.2 40.9 + - + +
162C GLY* 4.0 30.5 - - - -
163C THR* 4.7 1.8 - - - +
167C LEU* 3.7 6.6 + - + +
168C ASN* 1.4 74.1 + - - +
170C LEU* 1.4 65.8 + - - +
171C ARG 3.5 23.3 - - - +
172C ILE* 3.8 25.8 - - + -
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Residues in contact with LEU 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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6C ALA* 3.8 28.5 - - + -
141C ASN* 3.9 17.0 - - + +
142C ALA 2.8 16.0 + - - +
143C VAL* 4.2 7.6 - - + -
159C LYS* 4.5 2.6 + - - -
168C ASN* 3.2 24.3 + - - +
169C VAL* 1.4 72.1 - - - +
171C ARG* 1.3 64.4 + - - +
377C ALA* 3.9 18.8 - - - +
380C LEU* 4.2 28.3 - - + +
381C SER* 4.5 3.4 - - - +
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Residues in contact with ARG 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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142C ALA 4.0 0.6 + - - -
143C VAL* 3.4 9.9 - - + +
144C VAL 3.2 22.9 + - - -
159C LYS* 4.5 4.0 - - - +
169C VAL* 3.3 9.0 - - - +
170C LEU* 1.3 82.5 - - - +
172C ILE* 1.3 68.6 + - - +
173C ILE* 3.3 25.9 - - + +
177C THR* 5.7 3.8 - - - +
181C ILE* 5.3 4.4 - - - +
217C PHE* 6.0 3.4 - - - -
376C GLN* 3.3 37.8 + - - +
380C LEU* 3.7 25.7 - - + +
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Residues in contact with ILE 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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144C VAL* 3.3 21.1 - - + +
146C VAL* 3.6 32.3 - - + -
155C ARG* 4.5 21.1 + - + +
158C THR* 4.2 18.4 - - + +
159C LYS* 4.0 33.2 - - + +
169C VAL* 3.8 23.8 - - + -
171C ARG* 1.3 78.8 - - - +
173C ILE* 1.3 65.2 + - - +
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Residues in contact with ILE 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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143C VAL* 3.8 20.6 - - + -
144C VAL 3.2 4.0 + - - -
145C THR* 3.1 21.6 - - + -
146C VAL* 3.1 22.8 + - - -
155C ARG* 5.3 0.4 - - - +
171C ARG* 3.3 42.2 - - + +
172C ILE* 1.3 77.7 - - - +
174C ASN* 1.3 66.2 + - - +
177C THR* 4.9 8.1 - - + -
178C ALA* 3.8 29.4 - - + +
181C ILE* 4.7 5.6 - - + -
373C ALA* 4.2 4.0 - - - +
376C GLN* 4.2 20.0 - - + -
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Residues in contact with ASN 174 (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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146C VAL 3.3 5.3 - - - +
147C PRO 4.0 0.7 - - - +
148C ALA* 3.6 11.9 + - - +
155C ARG* 2.9 38.5 + - - +
173C ILE* 1.3 75.8 - - - +
175C GLU* 1.3 59.4 + - - +
176C PRO* 3.9 13.7 - - + -
177C THR* 3.2 20.0 + - - +
178C ALA* 3.0 26.9 + - - +
219C VAL* 3.4 27.5 - - - +
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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