Contacts of the helix formed by residues 315 - 325 (chain C) in PDB entry 3SAJ
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 315 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295C ASP* 3.7 22.7 + - - +
296C ILE* 3.4 29.9 - - + +
297C SER* 3.3 34.1 + - - +
313C TRP* 3.4 16.0 + - + +
314C GLY* 1.3 73.6 - - - +
316C GLY* 1.3 66.0 + - - +
317C ILE 3.2 3.4 - - - -
318C ASP* 3.0 28.5 + - - +
319C ILE* 3.4 12.1 + - - +
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Residues in contact with GLY 316 (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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87C HIS* 3.3 26.1 - - - +
89C CYS* 5.1 0.7 - - - -
103C PHE* 4.5 2.6 - - - -
313C TRP* 3.1 32.6 + - - -
315C GLN* 1.3 76.2 - - - +
317C ILE* 1.3 56.6 + - - +
319C ILE* 3.2 5.5 + - - +
320C GLN* 3.0 27.4 + - - +
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Residues in contact with ILE 317 (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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87C HIS* 4.8 9.6 + - + +
102C GLN* 4.1 13.0 - - - +
103C PHE* 3.8 26.4 - - + -
313C TRP 4.5 1.8 + - - -
314C GLY 4.2 13.1 + - - +
316C GLY* 1.3 76.8 - - - +
318C ASP* 1.3 68.1 + - - +
320C GLN* 3.7 17.8 - - - +
321C ARG* 3.0 29.5 + - + +
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Residues in contact with ASP 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU* 4.0 7.7 - - + +
294C ILE* 4.4 26.9 - - + +
296C ILE* 5.6 0.4 - - + -
314C GLY 4.8 1.0 - - - +
315C GLN* 3.0 28.1 + - + +
317C ILE* 1.3 86.6 - - - +
319C ILE* 1.3 63.6 + - + +
321C ARG* 3.4 23.1 + - - +
322C ALA* 3.1 28.2 + - - +
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Residues in contact with ILE 319 (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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65C TYR 3.9 17.0 - - - +
66C ALA* 5.0 0.2 - - + -
89C CYS* 4.7 5.8 - - + +
285C ALA* 5.0 0.2 - - - +
286C PHE* 3.9 22.2 - - + -
289C LEU* 3.7 27.1 - - + -
296C ILE* 3.5 28.3 - - + -
313C TRP* 3.9 18.6 - - + -
315C GLN 3.5 13.2 - - - +
316C GLY 3.2 7.9 + - - +
318C ASP* 1.3 80.7 - - + +
320C GLN* 1.3 65.4 + - - +
322C ALA* 3.3 2.3 + - - +
323C LEU* 3.0 43.6 + - + +
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Residues in contact with GLN 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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89C CYS* 3.5 22.0 - - - -
102C GLN* 3.0 58.2 + - - +
103C PHE* 3.6 23.8 - - + -
105C LEU* 5.1 1.3 - - + +
316C GLY 3.0 15.0 + - - +
317C ILE* 3.7 12.5 - - - +
319C ILE* 1.3 78.6 - - - +
321C ARG* 1.3 68.0 + - - +
323C LEU* 3.3 3.4 + - - +
324C GLN* 3.0 45.2 + - - +
339C GLU* 4.9 0.8 + - - +
341C GLY 6.0 0.2 - - - +
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Residues in contact with ARG 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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289C LEU* 5.7 1.4 - - - +
292C GLN* 4.8 6.7 + - - -
294C ILE* 4.0 24.9 - - - +
317C ILE* 3.0 19.7 + - + +
318C ASP* 3.8 19.2 + - - +
320C GLN* 1.3 86.5 + - - +
322C ALA* 1.3 65.2 + - - +
324C GLN* 3.2 6.8 + - - +
325C GLN* 3.0 66.0 + - + +
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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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285C ALA* 3.6 20.4 - - + +
288C SER* 5.4 4.9 - - - +
289C LEU* 3.6 31.4 - - + -
318C ASP 3.1 17.5 + - - +
319C ILE 3.7 4.5 - - - +
321C ARG* 1.3 81.1 - - - +
323C LEU* 1.3 61.6 + - - +
324C GLN 3.5 0.2 + - - -
325C GLN* 3.7 10.1 + - - +
326C VAL* 3.6 13.0 + - - +
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Residues in contact with LEU 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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66C ALA* 4.8 4.3 - - + -
89C CYS* 3.7 26.0 - - + -
91C ILE* 4.0 21.5 - - + -
105C LEU* 3.3 23.3 - - + +
281C VAL* 3.8 26.6 - - + +
282C MET* 3.9 12.8 - - + -
285C ALA* 3.6 21.8 - - + -
286C PHE* 5.6 3.6 - - + -
319C ILE* 3.0 37.5 + - + +
320C GLN 3.7 3.4 - - - +
321C ARG 3.2 0.2 - - - -
322C ALA* 1.3 77.5 - - - +
324C GLN* 1.3 60.9 + - - +
326C VAL* 3.6 15.1 - - - +
337C PHE* 3.9 5.5 - - - -
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Residues in contact with GLN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 4.0 8.7 - - + +
320C GLN* 3.0 32.8 + - - +
321C ARG* 3.2 6.8 + - - +
323C LEU* 1.3 78.4 - - - +
325C GLN* 1.3 76.0 + - - +
326C VAL 3.3 3.4 + - - -
337C PHE* 2.8 41.0 + - + +
338C ASN* 3.2 28.1 + - - +
339C GLU* 3.9 23.3 - - - +
341C GLY* 5.1 2.7 - - - +
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Residues in contact with GLN 325 (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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321C ARG* 3.0 58.8 + - + +
322C ALA* 3.7 5.6 + - - +
323C LEU 3.4 0.4 - - - -
324C GLN* 1.3 93.4 + - - +
326C VAL* 1.3 64.6 + - - +
327C ARG* 3.7 7.8 + - - +
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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