Contacts of the helix formed by residues 301 - 317 (chain C) in PDB entry 5I4A
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 301 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C PHE* 3.2 10.4 - - - +
300C SER* 1.3 83.6 + - - +
302C LYS* 1.3 64.1 + - - +
303C LYS* 3.5 12.7 + - - +
304C GLN* 3.0 23.4 + - - +
305C PHE* 3.2 16.5 + - - +
349C LEU* 3.6 13.4 - - - +
352C PRO* 5.8 0.2 - - - -
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Residues in contact with LYS 302 (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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301C SER* 1.3 72.9 - - - +
303C LYS* 1.3 63.2 + - - +
305C PHE* 3.2 14.2 + - + +
306C PHE* 3.1 45.7 + - + -
349C LEU* 3.9 26.4 - - + +
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Residues in contact with LYS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C SER* 3.2 11.0 + - - +
302C LYS* 1.3 78.7 - - - +
304C GLN* 1.3 62.9 + - - +
306C PHE* 3.1 11.0 + - - +
307C GLU* 3.0 47.7 + - + +
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Residues in contact with GLN 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PHE* 3.3 15.8 - - - +
300C SER* 2.9 33.0 + - - +
301C SER* 3.0 21.3 + - - +
303C LYS* 1.3 76.9 - - - +
305C PHE* 1.3 63.2 + - - +
307C GLU* 3.2 20.3 + - - +
308C VAL* 3.4 13.0 + - - +
375C LEU* 3.1 43.1 + - + +
376C LEU 3.8 1.6 + - - -
377C ASP* 2.8 32.1 + - - +
401C LYS* 4.2 16.6 - - + +
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Residues in contact with PHE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PHE* 3.7 42.1 - + + -
301C SER 3.2 10.1 + - - +
302C LYS* 3.2 19.1 + - + +
304C GLN* 1.3 79.1 - - - +
306C PHE* 1.3 91.4 + + - +
308C VAL* 3.2 5.2 + - - +
309C GLN* 2.9 51.8 + - + -
312C LEU* 3.7 17.5 - - + -
347C ALA* 5.2 8.1 - - + -
349C LEU* 6.2 0.2 - - + -
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LYS* 3.1 45.7 + - + -
303C LYS* 3.1 7.8 + - - +
305C PHE* 1.3 99.5 - + - +
307C GLU* 1.3 63.2 + - - +
308C VAL 3.4 0.3 + - - -
309C GLN* 3.5 32.6 + - - +
310C LYS 5.2 0.3 + - - -
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Residues in contact with GLU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C LYS* 3.0 48.0 + - + +
304C GLN* 3.5 13.5 - - - +
305C PHE 3.2 0.4 - - - -
306C PHE* 1.3 79.3 - - + +
308C VAL* 1.3 63.1 + - + +
309C GLN 3.5 0.2 - - - -
310C LYS* 5.2 1.4 + - - +
401C LYS* 3.5 29.7 + - - +
405C GLU* 4.1 15.2 - - - +
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Residues in contact with VAL 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PHE* 4.2 2.2 - - + -
304C GLN 3.5 15.5 - - - +
305C PHE 3.2 5.6 + - - +
307C GLU* 1.3 80.5 - - + +
309C GLN* 1.3 59.7 + - - +
310C LYS 3.2 3.1 - - - -
311C SER* 3.2 14.0 + - - +
312C LEU* 2.8 42.1 + - + +
375C LEU* 3.6 26.7 - - + -
401C LYS* 3.8 32.5 - - + +
404C LEU* 4.9 5.4 - - + -
405C GLU* 3.9 15.7 - - + +
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Residues in contact with GLN 309 (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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305C PHE* 2.9 42.8 + - + +
306C PHE* 3.5 31.6 + - - +
307C GLU 3.5 2.0 - - - -
308C VAL* 1.3 77.2 - - - +
310C LYS* 1.3 57.0 + - - +
312C LEU* 3.2 9.5 + - + +
313C LYS* 2.9 60.1 + - + +
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Residues in contact with LYS 310 (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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306C PHE 5.2 0.6 + - - -
307C GLU 5.2 1.9 + - - +
308C VAL 3.2 0.6 - - - -
309C GLN* 1.3 79.0 - - - +
311C SER* 1.3 63.8 + - - +
313C LYS* 3.2 10.4 + - - +
314C GLU* 2.9 51.6 + - + +
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Residues in contact with SER 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C VAL* 3.2 12.8 + - - -
310C LYS* 1.3 79.0 - - - +
312C LEU* 1.3 58.5 + - - +
314C GLU* 3.3 12.3 + - - +
315C LEU* 2.9 36.0 + - - +
404C LEU* 3.0 35.9 + - - -
405C GLU* 3.3 18.4 + - - -
407C ILE* 4.0 7.2 - - - +
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Residues in contact with LEU 312 (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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297C PHE* 4.4 7.6 - - + -
299C PHE* 3.5 41.1 - - + -
305C PHE* 3.7 21.8 - - + -
308C VAL* 2.8 33.3 + - + +
309C GLN* 3.5 7.2 - - + +
311C SER* 1.3 77.4 - - - +
313C LYS* 1.3 57.6 + - + +
315C LEU* 5.5 0.2 - - - -
316C PHE* 2.8 64.2 + - + +
317C HIS* 4.4 3.2 - - + +
375C LEU* 5.0 0.9 - - + -
404C LEU* 4.7 14.6 - - + -
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Residues in contact with LYS 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C GLN* 2.9 48.6 + - + +
310C LYS* 3.7 7.4 - - - +
312C LEU* 1.3 72.8 - - + +
314C GLU* 1.3 63.5 + - + +
317C HIS* 2.9 66.3 + - + +
318C ASN* 3.3 4.9 + - - +
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Residues in contact with GLU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LYS* 2.9 50.4 + - + +
311C SER* 3.7 7.3 + - - +
312C LEU 3.3 0.2 - - - -
313C LYS* 1.3 77.8 - - + +
315C LEU* 1.3 58.7 + - - +
318C ASN* 3.4 15.6 + - - +
321C SER* 3.2 18.2 - - - -
407C ILE* 3.6 23.5 - - + +
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Residues in contact with LEU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C SER 2.9 14.6 + - - +
314C GLU* 1.3 77.7 - - - +
316C PHE* 1.3 81.6 + - + +
318C ASN 4.5 0.2 - - - -
321C SER* 2.4 25.0 + - - +
322C VAL* 3.6 30.5 - - + -
323C PHE* 3.8 15.2 - - + +
324C TYR* 3.3 9.0 - - - -
404C LEU* 3.5 32.8 - - + -
407C ILE* 3.7 29.8 - - + -
412C ILE* 4.1 19.5 - - + -
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Residues in contact with PHE 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C PHE* 3.5 34.5 - + + -
312C LEU* 2.8 45.8 + - + +
315C LEU* 1.3 97.7 - - + +
317C HIS* 1.3 72.0 + - + +
318C ASN 3.5 1.3 - - - -
319C LYS* 4.6 3.8 - - - +
323C PHE* 3.7 41.3 - + - -
324C TYR* 2.6 24.1 + - - -
337C PHE* 3.4 30.4 - + + -
373C ILE* 4.6 7.2 - - + -
404C LEU* 4.6 7.4 - - + -
415C TYR* 5.9 2.7 - + - -
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Residues in contact with HIS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 4.4 3.5 - - + +
313C LYS* 2.9 54.0 + - + +
316C PHE* 1.3 83.5 - - + +
318C ASN* 1.3 59.9 + - - +
319C LYS* 3.4 15.1 + - - +
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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