Contacts of the strand formed by residues 180 - 183 (chain t) in PDB entry 6QX2
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 t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35t LEU* 4.4 5.2 - - - -
174t GLY 3.2 15.0 - - - +
175t ILE* 4.1 8.7 - - + -
176t ALA 4.2 0.4 - - - +
179t MET* 1.3 73.8 - - - +
181t THR* 1.3 63.9 + - - +
334t ASN* 3.0 24.7 + - - +
336t ILE* 3.3 17.5 - - - +
2017v G 3.9 28.7 + - - +
2018v C 4.4 7.6 + - - +
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Residues in contact with THR 181 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34t ALA 4.2 0.4 - - - +
35t LEU* 3.9 7.9 - - + -
36t PRO* 3.9 22.4 - - + -
43t LYS* 5.5 0.2 - - - -
172t ALA* 4.2 5.8 - - + +
173t SER* 3.3 9.2 - - - -
174t GLY* 2.8 49.6 + - - +
180t ALA* 1.3 76.6 - - - +
182t ASN* 1.3 63.7 + - - +
183t ILE* 3.7 11.6 - - - +
334t ASN* 3.3 12.2 + - - +
336t ILE 2.6 28.8 + - - -
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Residues in contact with ASN 182 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172t ALA 3.5 2.7 - - - -
173t SER* 3.4 21.3 - - - -
181t THR* 1.3 74.1 + - - +
183t ILE* 1.3 59.5 + - - +
267t GLN* 4.7 3.1 - - - +
331t PHE* 3.0 39.0 - - - +
332t GLY 2.9 31.1 + - - +
333t VAL* 3.5 8.1 - - - +
334t ASN* 2.8 41.9 + - + +
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Residues in contact with ILE 183 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36t PRO* 4.8 1.3 - - + -
167t LEU* 3.9 44.4 - - + +
168t LEU* 4.1 22.7 - - + -
171t GLY* 3.2 0.9 - - - -
172t ALA* 2.7 41.7 + - + +
181t THR* 3.7 18.8 - - - +
182t ASN* 1.3 76.1 - - - +
184t PRO* 1.3 79.3 - - + +
185t PRO* 3.9 1.2 - - - +
266t PHE* 5.8 0.5 - - - -
331t PHE* 3.8 5.7 - - - -
335t MET* 3.8 32.1 - - + -
336t ILE 4.3 7.6 - - - +
337t ALA* 4.9 0.9 - - + -
346t ILE* 5.9 0.7 - - + -
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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