Contacts of the helix formed by residues 312 - 324 (chain C) in PDB entry 4EEM
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 GLY 312 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307C TYR* 3.7 8.5 - - - -
311C GLY* 1.3 67.9 - - - -
313C GLU* 1.3 58.1 + - - +
314C ASP* 3.3 6.5 - - - -
315C ASP* 3.0 6.4 + - - +
316C ASP* 2.8 25.1 + - - +
355C ARG* 4.3 2.7 - - - -
359C ILE* 3.4 11.9 - - - +
2F NAG 3.0 38.1 + - - -
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Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ARG* 2.7 30.1 + - + +
225C ALA* 3.6 32.3 - - + +
304C PRO* 4.6 0.6 - - + +
307C TYR* 3.6 34.4 - - + +
311C GLY 3.2 11.1 + - - +
312C GLY* 1.3 71.3 + - - +
314C ASP* 1.3 59.8 + - - +
316C ASP* 3.0 6.1 + - - +
317C ILE* 2.9 34.4 + - + +
408C GOL 2.7 46.7 + - - -
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Residues in contact with ASP 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ARG* 4.3 4.7 - - - +
285C TYR* 3.8 4.2 - - - -
286C PHE* 4.0 11.8 - - - +
287C GLY* 3.5 33.4 + - - +
312C GLY 3.5 0.5 - - - -
313C GLU* 1.3 85.3 + - - +
315C ASP* 1.3 64.1 + - - -
317C ILE* 3.3 12.4 + - - +
318C PHE* 2.9 27.2 + - - +
408C GOL 3.3 17.0 + - - +
2F NAG 2.7 46.0 + - - -
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Residues in contact with ASP 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C TYR* 2.8 30.7 + - - -
284C GLN 4.4 5.5 - - - +
285C TYR* 4.9 1.4 - - - -
286C PHE 5.2 0.7 + - - -
312C GLY* 3.0 8.1 + - - +
314C ASP* 1.3 84.6 + - - +
316C ASP* 1.3 65.3 + - - +
318C PHE* 3.2 8.9 + - - +
319C ASN* 2.9 30.0 + - - +
359C ILE* 3.9 16.8 - - + -
1F MMA 4.1 8.6 - - - +
2F NAG 2.7 40.5 + - - +
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C PRO* 3.5 10.8 - - + +
307C TYR* 2.6 42.1 + - + +
312C GLY 2.8 6.6 + - - +
313C GLU 3.0 9.2 + - - +
315C ASP* 1.3 75.6 - - - +
317C ILE* 1.3 61.4 + - - +
319C ASN* 3.1 7.7 + - - +
320C ARG* 2.8 51.5 + - - +
358C ARG 4.2 0.9 - - - +
359C ILE* 4.1 2.6 - - + +
362C THR* 2.3 34.1 + - - +
365C THR* 4.8 3.8 + - - -
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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
----------------------------------------------------------
224C ARG* 5.2 2.9 - - - +
225C ALA* 4.9 5.2 - - + -
228C LEU* 5.2 4.9 - - + -
286C PHE* 3.8 26.0 - - + -
292C LEU* 5.3 0.4 - - + -
300C ILE* 4.5 3.1 - - + -
303C PHE* 3.3 63.3 - - + -
304C PRO* 4.0 11.2 - - + -
313C GLU* 2.9 23.2 + - + +
314C ASP* 3.5 13.7 - - - +
316C ASP* 1.3 74.9 - - - +
318C PHE* 1.3 63.8 + - - +
320C ARG* 3.2 11.2 + - - +
321C LEU* 3.0 28.2 + - + +
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Residues in contact with PHE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C VAL 5.4 0.9 - - - -
284C GLN* 3.4 70.4 - - + +
285C TYR 5.6 0.2 - - - -
286C PHE* 4.1 10.9 - - + -
314C ASP 2.9 14.8 + - - +
315C ASP* 3.2 10.5 + - - +
317C ILE* 1.3 76.9 - - - +
319C ASN* 1.3 78.3 + - - +
321C LEU* 3.2 12.4 + - - +
322C VAL* 3.0 47.2 + - + +
328C ILE* 3.7 32.8 - - + -
330C ARG* 5.9 0.4 - - - -
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Residues in contact with ASN 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLN* 5.5 0.5 - - - +
315C ASP* 2.9 20.9 + - - +
316C ASP* 3.4 5.4 - - - +
318C PHE* 1.3 90.1 - - - +
320C ARG* 1.3 53.3 + - - +
322C VAL* 3.1 5.9 + - - +
323C PHE* 2.7 56.4 + - + -
359C ILE* 3.1 37.2 + - - +
362C THR* 3.5 17.4 + - + -
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Residues in contact with ARG 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ILE* 3.1 33.3 + - + +
301C ASN 3.4 5.1 + - - -
302C GLY 2.9 31.0 + - - -
303C PHE* 3.9 0.6 - - - +
304C PRO* 3.4 32.5 - - - +
316C ASP* 2.8 30.7 + - - +
317C ILE* 3.3 13.5 - - - +
319C ASN* 1.3 75.5 - - - +
321C LEU* 1.3 57.7 + - - +
323C PHE* 3.3 1.7 + - - +
324C ARG* 2.9 27.4 + - - +
362C THR* 3.7 4.9 - - + +
365C THR* 4.6 4.4 + - - -
366C MET* 3.6 50.5 + - + +
369C ASP* 2.9 31.9 + - - +
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Residues in contact with LEU 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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266C PRO* 3.8 25.4 - - + -
286C PHE* 3.8 36.8 - - + -
292C LEU* 4.3 10.8 - - + -
296C GLN 4.7 1.1 - - - +
300C ILE* 3.8 21.8 - - + -
317C ILE* 3.0 22.3 + - + +
318C PHE* 3.2 6.9 + - - +
320C ARG* 1.3 75.4 - - - +
322C VAL* 1.3 61.8 + - + +
324C ARG* 3.1 7.4 + - - +
325C GLY 3.4 0.2 + - - -
326C MET* 2.9 57.4 + - + +
328C ILE* 4.0 14.8 - - + -
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Residues in contact with VAL 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C PHE* 3.0 50.4 + - + +
319C ASN* 3.7 7.2 - - - +
321C LEU* 1.3 76.7 - - + +
323C PHE* 1.3 68.7 + - + +
325C GLY* 3.0 20.1 + - - -
326C MET 3.9 15.8 - - - +
327C SER* 5.7 1.1 - - - -
328C ILE* 5.7 2.7 - - + -
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Residues in contact with PHE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ASN* 2.7 48.3 + - + +
320C ARG 3.8 4.3 - - - +
322C VAL* 1.3 82.3 - - + +
324C ARG* 1.3 79.4 + - - +
325C GLY 3.2 0.9 + - - -
359C ILE 5.8 0.9 - - - -
362C THR* 4.2 4.9 - - + -
363C LYS* 3.6 56.3 - - + -
366C MET* 4.3 5.4 - - - -
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Residues in contact with ARG 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C THR* 3.5 39.0 + - + +
300C ILE* 3.8 5.6 - - + -
320C ARG 2.9 18.3 + - - +
321C LEU 3.1 0.4 + - - -
322C VAL 3.1 1.0 - - - -
323C PHE* 1.3 104.0 + - - +
325C GLY* 1.3 60.3 + - - +
326C MET* 3.4 26.6 + - + +
363C LYS* 5.4 5.3 + - - +
366C MET* 3.8 24.0 - - + +
367C LEU* 3.5 30.1 - - - +
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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