Contacts of the strand formed by residues 150 - 154 (chain D) in PDB entry 6APL
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 ARG 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299B ASP* 5.6 1.0 + - - -
348B TYR* 3.6 44.2 + - - +
349B ALA 5.4 2.9 + - - -
66D CYS 5.0 0.4 - - - +
69D LEU* 4.2 21.9 - - - +
148D CYS* 3.0 39.2 - - - +
149D ILE* 1.3 74.3 - - - +
151D CYS* 1.3 59.7 + - - +
172D HIS* 3.4 8.6 - - + +
173D ASP* 2.9 53.1 + - - +
174D TYR 3.2 6.4 + - - -
318D ASP* 5.8 0.4 - - + -
319D GLN* 3.6 37.0 - - + +
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Residues in contact with CYS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D PHE* 4.1 6.5 - - - -
149D ILE* 3.6 16.8 - - - -
150D ARG* 1.3 74.6 - - - +
152D ALA* 1.3 60.5 + - - +
172D HIS* 3.4 8.9 - - - -
174D TYR* 3.3 11.0 - - - +
176D PHE* 3.9 20.0 - - + -
313D ALA* 4.5 1.3 - - + -
317D CYS* 2.0 51.1 - - + -
319D GLN 3.0 8.0 + - - +
320D VAL* 3.3 9.5 - - + -
321D SER 2.9 22.9 + - - -
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D CYS* 1.3 74.5 - - - +
153D VAL* 1.3 56.2 + - - +
154D VAL* 4.1 0.9 - - + -
169D ILE* 4.0 15.7 - - + +
172D HIS* 3.7 26.5 - - + +
174D TYR 2.9 8.8 + - - +
175D VAL* 3.3 7.3 - - + +
176D PHE* 2.6 35.9 + - - +
321D SER 3.3 7.9 - - - +
323D TYR* 4.1 14.1 - - + -
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Residues in contact with VAL 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA* 1.3 77.4 - - - +
154D VAL* 1.3 62.4 + - - +
176D PHE* 3.6 20.4 - - + +
178D LEU* 4.4 3.4 - - + -
309D MSE 4.0 6.7 - - + +
310D LEU* 3.8 31.4 - - + +
313D ALA* 3.6 31.4 - - + -
320D VAL* 5.1 3.4 - - + -
321D SER 2.8 14.2 + - - +
322D ALA* 3.5 2.3 - - - -
323D TYR* 2.9 27.9 + - - +
325D PHE* 3.5 27.6 - - + -
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA 4.8 0.7 - - - -
153D VAL* 1.3 74.6 - - - +
155D GLY* 1.3 73.1 + - - +
156D ASN* 4.1 7.0 - - - +
160D LEU* 3.7 18.8 - - + -
169D ILE* 3.9 35.7 - - + -
175D VAL* 4.0 7.4 - - + -
176D PHE 2.9 19.3 + - - +
177D ARG* 3.8 30.3 - - + +
178D LEU* 3.6 22.2 - - - +
190D VAL* 4.5 7.4 - - + -
323D TYR* 3.3 5.2 - - + -
325D PHE* 4.3 1.3 - - - -
337D TYR* 5.1 2.0 - - + +
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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