Contacts of the strand formed by residues 319 - 323 (chain C) 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 GLN 319 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C LEU* 5.4 8.5 - - + -
70C LEU* 4.5 9.9 - - + -
149C ILE 3.3 1.7 + - - +
150C ARG* 3.4 51.3 - - + +
151C CYS 3.0 24.9 + - - +
172C HIS* 3.5 18.3 + - - -
317C CYS* 3.3 2.9 - - - +
318C ASP* 1.3 80.1 - - + +
320C VAL* 1.3 72.3 + - - +
321C SER* 3.7 16.0 + - - -
368C ILE 5.5 0.9 - - - +
370C GLN* 5.1 5.1 - - - +
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Residues in contact with VAL 320 (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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70C LEU* 5.0 2.0 - - + -
151C CYS* 3.2 7.4 - - + +
153C VAL* 4.8 1.3 - - + -
310C LEU* 3.9 11.2 - - + -
313C ALA* 3.3 44.6 - - + +
314C LEU* 3.6 31.2 - - + +
317C CYS* 3.9 5.6 - - + -
319C GLN* 1.3 86.1 + - - +
321C SER* 1.3 62.6 + - - +
368C ILE 4.9 3.6 + - - -
369C LEU* 3.5 23.7 - - + -
370C GLN 3.3 18.5 + - - -
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Residues in contact with SER 321 (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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151C CYS 2.9 6.6 + - - -
152C ALA* 3.4 0.5 - - - -
153C VAL* 2.8 32.6 + - - +
172C HIS* 2.9 29.7 + - - -
319C GLN* 3.7 9.5 + - - -
320C VAL* 1.3 77.8 + - - +
322C ALA* 1.3 58.1 + - - +
323C TYR* 3.5 21.7 + - - -
369C LEU* 4.1 1.1 - - - -
370C GLN* 3.2 18.9 - - - +
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Residues in contact with ALA 322 (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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153C VAL* 3.6 5.2 - - - -
310C LEU* 4.1 13.0 - - + -
321C SER* 1.3 71.5 - - - +
323C TYR* 1.3 60.0 + - - +
325C PHE* 3.9 15.7 - - + -
369C LEU* 3.5 21.6 - - + +
370C GLN 2.7 9.7 + - - +
371C LEU* 3.7 21.7 - - + +
372C TYR* 2.8 34.0 + - - +
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Residues in contact with TYR 323 (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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152C ALA* 4.0 14.4 - - + -
153C VAL 2.9 11.7 + - - +
154C VAL* 3.3 5.5 - - + -
155C GLY 2.7 32.7 + - - +
160C LEU* 3.8 9.2 - - + -
165C GLN* 3.6 28.9 - - + -
168C ASN* 3.7 15.3 + - + +
169C ILE* 3.5 43.5 - - + -
172C HIS* 3.4 19.1 - + - -
321C SER* 3.5 31.2 + - - -
322C ALA* 1.3 73.9 - - - +
324C GLY* 1.3 55.3 + - - +
325C PHE* 3.5 2.7 - - - -
370C GLN* 6.1 1.1 - - + +
372C TYR* 3.8 23.1 - + + -
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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