Contacts of the strand formed by residues 361 - 368 (chain A) in PDB entry 2F24
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 GLU 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A SER* 2.8 25.4 + - - +
13A PHE 3.2 9.9 - - - +
14A GLN* 3.2 28.3 + - + +
20A TYR* 5.0 4.1 - - - +
355A GLU* 3.5 6.1 - - - +
356A ALA* 2.9 31.6 + - - +
357A ASN* 4.6 15.9 + - - +
359A TYR 3.3 3.2 + - - -
360A GLU* 1.3 94.7 + - + +
362A ILE* 1.3 68.2 + - - +
363A VAL* 4.1 10.8 - - + +
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Residues in contact with ILE 362 (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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11A SER* 3.7 1.2 - - - -
12A VAL* 3.0 26.0 + - - +
13A PHE* 2.9 30.1 + - + +
20A TYR* 3.9 15.0 - - + +
21A ARG* 3.9 24.7 - - - +
23A PRO* 4.0 13.5 - - + -
38A ALA* 3.6 30.7 - - + -
353A LEU* 3.7 31.0 - - + -
354A TYR 3.3 9.4 - - - +
355A GLU* 4.6 9.4 - - + -
361A GLU* 1.3 77.2 - - - +
363A VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 4.0 21.3 - - + -
10A GLU 3.6 12.8 - - - +
11A SER* 4.0 16.4 - - - +
352A CYS 3.5 1.6 - - - +
353A LEU* 3.3 7.4 - - - -
354A TYR* 2.8 64.8 + - + +
356A ALA* 4.0 24.5 - - + -
361A GLU* 4.1 9.2 - - + +
362A ILE* 1.3 76.5 - - - +
364A PHE* 1.3 71.3 + - - +
365A LEU* 4.6 0.2 - - + -
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Residues in contact with PHE 364 (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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8A GLN* 3.8 28.0 - - + -
9A LYS* 3.3 4.5 - - - -
10A GLU 2.8 41.8 + - - +
12A VAL* 4.0 12.1 - - + -
25A LEU* 4.3 4.0 - - + -
34A LEU* 3.5 32.5 - - + -
66A VAL* 3.9 11.4 - - + -
68A TRP* 3.5 24.2 - + - -
351A GLY* 3.8 14.1 - - - -
352A CYS 3.3 9.2 - - - -
353A LEU* 4.0 17.5 - - + +
362A ILE 4.2 0.4 + - - -
363A VAL* 1.3 73.7 - - - +
365A LEU* 1.3 72.6 + - - +
366A MET* 3.8 27.4 - - + -
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Residues in contact with LEU 365 (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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6A VAL* 4.5 14.8 - - + -
8A GLN 3.2 4.0 - - - +
9A LYS* 3.5 43.3 - - + -
327A LEU* 4.0 44.2 - - + +
350A PHE 3.8 0.3 - - - +
351A GLY* 3.4 2.9 - - - -
352A CYS* 2.8 44.8 + - + +
354A TYR* 3.3 33.4 - - + +
363A VAL* 4.6 0.2 - - + -
364A PHE* 1.3 77.3 - - - +
366A MET* 1.3 59.8 + - - +
367A PHE* 4.2 9.7 - - + -
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Residues in contact with MET 366 (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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6A VAL* 3.6 3.0 - - - +
7A LEU* 2.8 37.5 + - + +
8A GLN* 2.9 31.5 + - + +
59A TYR* 3.8 14.6 - - + -
64A HIS 3.3 28.0 - - - +
65A GLN* 4.0 2.0 - - - -
66A VAL* 3.9 8.1 - - + -
340A MET* 3.7 30.3 - - - +
349A LEU* 3.7 21.8 - - + -
350A PHE 3.2 13.9 - - - +
364A PHE* 3.8 13.2 - - + -
365A LEU* 1.3 74.8 - - - +
367A PHE* 1.3 63.5 + - - +
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Residues in contact with PHE 367 (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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3A SER* 3.6 22.9 - - - +
6A VAL* 4.1 7.0 - - + -
7A LEU* 4.4 2.2 - - - +
294A LEU* 4.3 15.0 - - + -
309A ALA* 4.8 5.2 - - + -
327A LEU* 4.1 31.2 - - + -
337A LEU* 4.8 4.3 - - + -
349A LEU* 3.7 2.8 - - - +
350A PHE* 2.8 60.4 + + + +
352A CYS* 4.3 17.3 - - + -
365A LEU* 4.4 8.7 - - + -
366A MET* 1.3 82.7 - - - +
368A THR* 1.3 75.8 + - - +
371A GLN* 3.1 13.5 - - - +
372A ALA* 3.9 21.1 - - + -
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Residues in contact with THR 368 (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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7A LEU* 4.0 13.9 - - + -
343A GLY* 4.1 9.4 - - - -
344A PRO* 4.4 1.3 - - + -
345A ASP* 2.6 32.7 + - - +
347A SER* 3.2 12.7 + - - -
348A PRO 3.1 10.1 - - - +
349A LEU* 3.9 18.2 - - + -
350A PHE* 4.3 0.9 - - - -
367A PHE* 1.3 87.5 - - - +
369A LEU* 1.3 65.2 + - - +
371A GLN* 2.9 26.2 + - - +
372A ALA 3.1 18.0 + - - -
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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