Contacts of the strand formed by residues 180 - 183 (chain A) in PDB entry 6FQS
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 ALA 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.5 4.3 - - - -
174A GLY 3.2 15.0 - - - +
175A ILE* 4.0 15.7 - - + -
176A ALA* 4.2 2.5 - - - +
179A MET* 1.3 76.5 - - - +
181A THR* 1.3 66.8 + - - +
334A ASN* 3.0 23.4 + - - +
336A ILE* 3.8 15.6 - - - +
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Residues in contact with THR 181 (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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35A LEU* 3.8 19.1 - - + -
36A PRO* 3.9 17.0 - - + -
172A ALA* 4.6 4.5 - - + -
173A SER* 3.3 8.1 - - - -
174A GLY* 2.8 47.2 + - - +
180A ALA* 1.3 77.8 - - - +
182A ASN* 1.3 65.4 + - - +
183A ILE* 3.8 8.7 - - - +
334A ASN* 3.1 6.9 + - - +
336A ILE* 2.6 36.7 + - - -
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Residues in contact with ASN 182 (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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172A ALA 3.4 2.1 - - - +
173A SER* 3.2 22.2 - - - -
181A THR* 1.3 74.5 + - - +
183A ILE* 1.3 59.5 + - - +
184A PRO* 4.1 0.3 - - - +
267A GLN* 4.8 2.5 + - - +
331A PHE* 3.3 33.3 - - - -
332A GLY 2.8 31.5 + - - +
333A VAL* 3.5 8.7 - - - +
334A ASN* 2.8 40.6 + - + +
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Residues in contact with ILE 183 (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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36A PRO* 4.5 0.2 - - + -
167A LEU* 3.7 36.8 - - + +
168A LEU* 3.9 24.7 - - + -
171A GLY* 3.1 9.2 - - - -
172A ALA* 2.7 46.3 + - + +
181A THR* 3.8 14.8 - - - +
182A ASN* 1.3 76.6 + - - +
184A PRO* 1.3 75.1 - - + +
185A PRO* 3.9 1.0 - - - +
266A PHE* 5.8 0.5 - - - -
331A PHE* 4.1 4.8 - - - -
335A MET* 3.7 31.4 - - + -
336A ILE 4.2 9.6 - - - +
337A ALA* 5.0 0.4 - - + -
346A ILE* 6.2 0.4 - - + -
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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