Contacts of the strand formed by residues 316 - 321 (chain A) in PDB entry 4TR8
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 LEU 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A LYS* 3.9 25.6 - - + -
284A LEU 3.5 2.6 - - - +
285A GLN* 3.6 0.9 - - - -
286A LEU* 2.7 46.0 + - + +
311A TYR* 3.9 13.7 - - - +
314A GLY 3.3 0.6 + - - -
315A ASN* 1.3 76.8 - - - +
317A GLU* 1.3 73.7 + - - +
318A ILE* 4.6 8.2 - - + +
341A LEU* 4.1 29.6 - - + -
342A SER 4.0 8.5 - - - +
343A ASP* 3.9 7.9 - - - +
344A SER* 3.6 28.7 - - - +
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Residues in contact with GLU 317 (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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283A ARG* 3.2 44.6 + - + -
284A LEU 3.3 7.9 - - - +
285A GLN* 4.0 26.5 + - + +
316A LEU* 1.3 73.8 - - - +
318A ILE* 1.3 63.6 + - - +
344A SER* 3.1 26.3 - - - -
366A ARG* 3.7 17.0 + - - +
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Residues in contact with ILE 318 (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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283A ARG* 4.7 0.4 - - - -
284A LEU* 2.7 57.5 + - + +
286A LEU* 4.8 2.7 - - + -
316A LEU* 4.6 16.8 - - + -
317A GLU* 1.3 77.1 - - - +
319A GLY* 1.3 59.9 + - - +
320A PHE* 3.5 35.0 - - + -
341A LEU* 4.6 20.0 - - + -
343A ASP 3.5 23.1 - - - +
344A SER* 3.7 16.2 - - - +
346A SER 3.8 13.2 - - - +
364A PRO* 3.8 9.6 - - + -
366A ARG* 4.4 6.7 - - - +
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Residues in contact with GLY 319 (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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282A ILE 3.3 10.3 - - - -
283A ARG* 4.5 1.3 - - - -
318A ILE* 1.3 76.1 - - - +
320A PHE* 1.3 63.8 + - - -
344A SER 5.1 0.4 + - - -
364A PRO* 3.3 10.2 - - - +
365A MET* 2.8 36.8 + - - -
366A ARG* 3.9 18.4 - - - +
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Residues in contact with PHE 320 (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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281A GLY* 3.5 0.3 - - - -
282A ILE* 2.8 36.2 + - - +
284A LEU* 4.0 25.8 - - + -
318A ILE* 3.5 43.1 - - + -
319A GLY* 1.3 75.9 - - - -
321A ASN* 1.3 62.6 + - - +
322A VAL 3.3 1.0 + - - -
325A LEU* 3.8 30.3 - - + -
339A PHE* 5.9 2.7 - + - -
341A LEU* 4.5 3.6 - - + -
348A ALA* 3.6 23.3 - - + -
362A VAL* 3.5 42.8 - - + -
363A MET 3.8 0.4 - - - -
364A PRO* 3.7 17.0 - - + -
365A MET* 3.6 12.2 - - - +
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Residues in contact with ASN 321 (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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278A LYS 5.3 2.0 + - - -
279A TYR 3.7 19.6 + - - +
280A ARG* 3.5 12.0 - - - +
320A PHE* 1.3 71.6 - - - +
322A VAL* 1.3 64.3 + - - +
323A SER* 2.8 30.5 + - - -
324A TYR* 3.2 59.6 + - + +
325A LEU* 3.4 8.0 + - - +
363A MET 5.4 1.6 + - - +
365A MET* 3.6 15.5 - - + +
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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