Contacts of the helix formed by residues 305 - 313 (chain A) in PDB entry 5C53
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 SER 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A LEU* 1.3 75.7 - - - +
306A SER* 1.3 59.3 + - - +
307A PHE* 3.7 8.5 + - - +
308A GLN* 3.0 33.7 + - - +
309A ARG* 2.8 25.7 + - - +
849A THR* 4.5 4.0 - - - +
850A ILE* 6.4 1.1 - - - -
1083A LEU* 5.1 9.9 - - - +
1092A PHE* 5.8 0.3 - - - -
1095A SER* 5.2 4.5 + - - -
6T T 3.6 25.5 + - - -
7T A 3.3 9.2 - - - -
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Residues in contact with SER 306 (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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305A SER* 1.3 70.1 - - - +
307A PHE* 1.3 62.6 + - - +
309A ARG* 3.1 27.7 + - - +
310A SER* 2.9 27.9 + - - -
6T T 4.9 7.8 + - - -
7T A 2.7 29.1 + - - -
8T C 5.7 0.9 - - - -
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER* 3.2 8.4 - - - +
306A SER* 1.3 82.3 + - - +
308A GLN* 1.3 60.6 + - + +
310A SER* 2.3 29.5 + - - -
311A LEU* 3.3 33.7 - - + +
1092A PHE* 3.9 32.3 - + - -
6T T 5.4 5.4 - - - +
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Residues in contact with GLN 308 (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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304A LEU* 3.3 18.9 - - + +
305A SER* 3.0 38.3 + - - +
307A PHE* 1.3 76.9 - - + +
309A ARG* 1.3 59.1 + - - +
311A LEU* 3.3 11.9 - - - +
312A TRP* 2.9 31.3 + - - +
347A TRP* 3.5 35.0 - - + -
1082A ALA* 3.3 26.5 + - - +
1083A LEU* 3.3 25.5 - - - +
1092A PHE* 3.5 19.2 - - + -
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Residues in contact with ARG 309 (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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299A MET* 3.7 11.5 - - - +
304A LEU* 3.3 30.0 + - + +
305A SER 2.8 16.5 + - - +
306A SER* 3.3 36.3 - - - +
308A GLN* 1.3 76.6 - - - +
310A SER* 1.3 63.0 + - - +
312A TRP* 4.0 7.0 - - - -
313A ILE* 3.2 32.3 + - + +
353A VAL* 4.2 21.5 - - + -
354A ASN* 3.5 27.9 - - - +
849A THR* 2.9 23.8 + - - -
7T A 3.4 16.6 + - - -
8T C 5.0 6.3 + - - -
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Residues in contact with SER 310 (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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306A SER 2.9 10.9 + - - -
307A PHE* 2.3 39.2 + - - -
309A ARG* 1.3 78.4 - - - +
311A LEU* 1.3 59.2 + - - +
313A ILE* 3.4 21.7 - - - +
314A ALA* 3.6 9.5 + - - +
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Residues in contact with LEU 311 (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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307A PHE* 3.3 40.6 - - + +
308A GLN* 3.3 22.7 - - + +
310A SER* 1.3 76.0 - - - +
312A TRP* 1.3 63.3 + - - +
313A ILE 3.4 0.7 - - - -
314A ALA* 3.5 21.0 + - + +
315A ALA* 3.6 7.3 + - - +
344A SER 5.6 1.1 - - - +
345A TRP* 6.0 7.6 - - + +
347A TRP* 3.5 29.2 - - + -
348A LEU* 4.7 4.4 - - + +
1092A PHE* 5.6 2.7 - - + -
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Residues in contact with TRP 312 (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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304A LEU* 3.8 20.6 - - + -
308A GLN 2.9 19.6 + - - +
309A ARG* 3.3 9.6 + - - +
311A LEU* 1.3 78.6 - - - +
313A ILE* 1.3 80.0 + - + +
314A ALA 3.1 1.1 - - - -
315A ALA* 3.3 21.5 + - - +
347A TRP* 4.0 9.0 - + + -
348A LEU* 3.3 34.8 + - + +
351A SER 3.0 20.3 + - - -
352A SER* 3.5 26.2 - - - +
353A VAL* 4.4 16.2 - - + -
358A GLU* 3.3 30.7 - - - -
361A ARG* 4.2 16.4 - - - -
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Residues in contact with ILE 313 (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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309A ARG* 3.3 19.3 - - + +
310A SER* 3.4 13.7 - - - +
312A TRP* 1.3 93.8 - - + +
314A ALA* 1.3 65.6 + - - +
315A ALA 3.1 3.7 + - - +
316A LYS* 4.0 21.7 + - - +
353A VAL* 5.0 14.8 - - + -
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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