Contacts of the helix formed by residues 312 - 327 (chain C) in PDB entry 5G04
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 MET 312 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C LEU* 4.3 25.6 - - + -
307C LEU* 3.0 52.7 + - + +
310C ARG* 3.2 27.3 + - - +
311C SER* 1.3 68.4 - - - +
313C LYS* 1.3 64.9 + - - +
314C SER* 3.3 3.6 - - - +
315C GLU* 3.8 31.0 - - + +
316C LEU* 3.1 6.6 + - - +
343C LEU* 4.0 3.1 - - - +
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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
----------------------------------------------------------
311C SER 3.1 10.8 + - - +
312C MET* 1.3 68.9 - - - +
314C SER* 1.3 52.4 - - - +
316C LEU* 3.1 5.9 + - - +
317C SER* 2.4 42.0 + - - +
340C TYR* 5.1 2.2 - - + +
343C LEU* 3.4 53.6 + - + +
344C ARG* 3.9 24.4 + - + +
345C SER* 5.7 1.0 - - - -
27M GLU* 4.0 24.0 - - - +
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Residues in contact with SER 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C MET* 5.0 2.7 - - - -
313C LYS* 1.3 78.2 - - - +
315C GLU* 1.3 67.3 + - - +
317C SER* 3.1 7.5 + - - -
318C TYR* 3.0 20.8 + - - +
285J PHE* 3.8 17.7 - - - -
286J TYR* 4.6 6.1 - - - -
289J HIS* 2.9 55.9 + - - +
27M GLU* 5.0 0.4 + - - -
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Residues in contact with GLU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ASN* 5.4 10.5 + - - +
307C LEU* 3.9 18.0 - - + +
312C MET* 3.3 37.2 + - + +
314C SER* 1.3 82.6 - - - +
316C LEU* 1.3 62.4 + - - +
318C TYR* 3.3 12.4 + - - +
319C LEU* 3.1 21.5 + - - +
286J TYR* 2.8 40.5 + - + -
289J HIS* 6.0 0.2 - - - +
290J LYS* 3.9 14.2 + - - +
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C SER* 3.3 31.0 - - - +
307C LEU* 3.4 22.8 - - + +
308C TYR* 4.0 19.1 - - + +
312C MET 3.1 10.1 + - - +
313C LYS* 3.3 8.7 - - - +
315C GLU* 1.3 75.6 - - - +
317C SER* 1.3 51.5 + - - +
319C LEU* 2.9 13.6 + - + +
320C ALA* 2.6 36.5 + - - +
336C VAL* 4.7 4.3 - - + +
339C ASN* 3.8 23.1 - - + +
340C TYR* 3.9 18.2 - - + +
343C LEU* 3.9 22.9 - - + -
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Residues in contact with SER 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LYS 2.4 26.9 + - - -
314C SER 3.4 5.4 - - - -
316C LEU* 1.3 70.8 - - - +
318C TYR* 1.3 64.8 + - - +
320C ALA* 4.1 1.8 - - - -
321C HIS* 3.3 28.8 + - - +
340C TYR* 3.3 24.8 - - - -
282J ASN* 3.7 1.2 - - - +
285J PHE* 3.8 17.6 - - - -
27M GLU* 2.8 29.5 + - - -
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Residues in contact with TYR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ARG* 4.9 11.0 - - - -
314C SER 3.0 8.6 + - - +
315C GLU* 3.5 12.8 - - - +
316C LEU 3.2 0.2 - - - -
317C SER* 1.3 76.8 - - - +
319C LEU* 1.3 62.5 + - - +
322C ASN* 3.2 30.3 + - - +
282J ASN* 3.1 47.4 + - - +
283J GLU* 3.1 27.4 + - - -
285J PHE* 4.4 3.3 - - + -
286J TYR* 3.5 62.3 - + + -
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Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ARG* 3.4 49.4 - - - +
300C MET* 3.7 21.3 - - + +
303C PHE* 4.3 7.4 - - + -
304C SER* 4.0 22.2 - - - +
307C LEU* 3.9 23.1 - - + -
315C GLU 3.1 11.6 + - - +
316C LEU* 2.9 21.5 + - + +
318C TYR* 1.3 76.2 - - - +
320C ALA* 1.3 55.7 + - - +
322C ASN* 3.4 3.8 - - - +
323C LEU* 3.0 36.5 + - + +
336C VAL* 4.0 11.2 - - + -
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LEU 2.6 17.9 + - - +
317C SER* 4.3 2.5 - - - +
319C LEU* 1.3 71.0 - - - +
321C HIS* 1.3 66.6 + - + +
323C LEU* 3.1 13.0 + - - +
324C CYS* 3.1 14.7 + - - +
336C VAL* 3.7 17.5 - - + +
337C ILE* 4.0 9.3 - - + +
340C TYR* 3.7 40.6 - - + -
24M LEU* 4.2 4.5 - - + -
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Residues in contact with HIS 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C SER* 3.3 22.3 + - - +
320C ALA* 1.3 79.5 - - + +
322C ASN* 1.3 62.4 + - - +
324C CYS* 3.6 1.9 + - - +
325C GLU* 3.0 32.3 + - - +
340C TYR* 3.7 27.3 + + - -
282J ASN* 3.1 32.4 - - + +
285J PHE* 6.2 5.6 - + + +
308J TYR* 5.3 1.3 - - - -
24M LEU* 3.4 28.7 - - + +
25M PRO 3.8 11.6 + - - -
26M TYR* 4.0 34.1 - + - -
27M GLU* 4.6 10.5 - - + +
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Residues in contact with ASN 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ARG* 3.7 26.5 - - - +
294C PRO* 4.8 4.8 + - - +
295C TYR* 5.7 3.4 - - - -
318C TYR* 3.2 33.9 + - - +
319C LEU 3.4 6.1 - - - +
321C HIS* 1.3 74.5 - - - +
323C LEU* 1.3 63.6 + - - +
325C GLU* 3.3 10.6 + - - +
326C ILE* 3.2 34.2 + - - +
282J ASN* 2.7 18.7 + - - +
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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
----------------------------------------------------------
290C ARG* 3.7 20.6 - - - +
296C ARG 4.4 5.6 - - - +
297C ILE* 3.9 30.3 - - + -
300C MET* 3.8 19.7 - - + -
319C LEU* 3.0 18.4 + - + +
320C ALA 3.1 5.3 + - - +
322C ASN* 1.3 73.8 - - - +
324C CYS* 1.3 62.3 + - - +
326C ILE* 2.9 31.8 + - + +
327C ASP 3.0 17.2 + - - +
333C THR* 3.9 16.6 - - - +
336C VAL* 3.7 38.6 - - + -
337C ILE* 4.9 0.2 - - + -
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Residues in contact with CYS 324 (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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320C ALA 3.1 6.9 + - - +
321C HIS 3.8 2.9 - - - +
322C ASN 3.4 0.2 - - - -
323C LEU* 1.3 77.4 - - - +
325C GLU* 1.3 64.0 + - - +
326C ILE 4.4 0.2 - - - -
327C ASP 4.6 1.8 - - - -
328C LYS* 3.1 69.1 + - - +
333C THR* 4.1 5.7 + - - -
337C ILE* 4.1 17.3 - - + -
353C TYR* 5.7 5.4 - - - -
23M LYS* 6.6 0.2 - - - -
24M LEU* 3.6 37.9 - - + -
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Residues in contact with GLU 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 HIS* 3.0 27.3 + - - +
322C ASN* 3.3 12.2 + - - +
323C LEU 3.2 0.2 - - - -
324C CYS* 1.3 83.4 - - - +
326C ILE* 1.3 62.0 + - + +
328C LYS* 5.1 2.9 + - - +
282J ASN* 4.4 14.6 + - - +
24M LEU* 5.1 2.1 - - - +
100P ASP* 5.1 1.9 - - - +
129P LYS* 3.3 33.7 + - + +
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Residues in contact with ILE 326 (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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290C ARG* 4.5 0.2 - - - +
294C PRO 3.8 16.4 - - - +
295C TYR* 3.5 55.9 - - + +
297C ILE* 5.2 7.4 - - + -
322C ASN* 3.2 27.8 + - - +
323C LEU* 2.9 27.3 + - + +
324C CYS 4.4 0.2 - - - -
325C GLU* 1.3 81.4 - - + +
327C ASP* 1.3 64.2 + - + +
98P GLU* 6.4 1.6 - - + -
100P ASP* 3.7 26.7 - - + +
101P ARG 5.7 0.2 - - - +
129P LYS* 5.1 4.2 - - - +
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ILE* 4.0 18.0 - - + +
323C LEU 3.0 11.8 + - - +
326C ILE* 1.3 77.6 - - + +
328C LYS* 1.3 62.3 + - - +
329C TYR* 3.8 12.3 + - - +
330C ARG* 3.0 34.9 - - - +
333C THR* 2.9 27.4 + - - +
98P GLU* 6.6 0.2 - - - -
132P ASP* 4.8 7.0 - - - +
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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
------------------------------------------------------------
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