Contacts of the helix formed by residues 307 - 320 (chain C) in PDB entry 5JLH
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 307 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C VAL* 4.2 14.5 - - - +
220C LEU* 4.6 8.8 - - - +
305C TYR 3.3 0.6 + - - -
306C PRO* 1.3 72.9 - - - +
308C ILE* 1.3 63.9 + - - +
309C ALA 3.3 3.6 - - - -
310C ASP* 3.4 19.6 + - - +
311C ARG* 3.1 22.3 + - - +
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Residues in contact with ILE 308 (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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218C VAL* 3.5 24.5 - - + -
260C LEU* 5.1 6.1 - - + -
261C PHE* 4.5 9.9 - - + -
273C ILE* 5.1 5.4 - - + -
298C LEU* 4.1 15.3 - - + -
302C THR 3.9 3.4 - - - +
303C THR* 3.1 46.0 - - + +
305C TYR* 3.4 33.7 + - + +
306C PRO 3.4 0.8 + - - -
307C GLY* 1.3 77.4 - - - +
309C ALA* 1.3 65.0 + - - +
311C ARG* 3.2 4.7 + - - +
312C MET* 2.9 37.3 + - + +
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Residues in contact with ALA 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LEU* 4.4 8.4 - - + +
307C GLY 3.3 0.8 - - - -
308C ILE* 1.3 81.4 - - - +
310C ASP* 1.3 61.6 + - - +
312C MET* 3.3 5.4 + - - +
313C GLN* 2.9 32.0 + - - +
328C ILE* 3.9 13.3 - - + +
330C ALA* 4.3 24.0 - - + -
334C ARG* 5.2 4.9 - - - +
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Residues in contact with ASP 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU* 4.3 28.9 - - + +
307C GLY* 3.4 18.7 + - - +
308C ILE 3.2 0.4 - - - -
309C ALA* 1.3 80.7 - - - +
311C ARG* 1.3 59.1 - - - +
313C GLN* 3.2 13.1 + - - +
314C LYS* 2.9 29.3 + - - +
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Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C VAL* 3.5 19.5 - - + -
219C ALA 3.3 27.0 + - - +
220C LEU* 5.1 3.1 - - - +
221C ASP* 4.1 1.8 + - - +
222C PHE* 3.9 17.8 - - - +
258C GLU* 3.1 26.0 + - - -
261C PHE* 3.4 24.4 - - + +
262C GLN* 4.5 8.5 - - - +
274C HIS* 5.5 0.2 - - - -
307C GLY 3.1 11.4 + - - +
308C ILE 3.7 5.8 - - - +
310C ASP* 1.3 80.0 - - - +
312C MET* 1.3 63.8 + - - +
314C LYS* 3.2 39.8 + - - +
315C GLU* 2.8 54.2 + - - +
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Residues in contact with MET 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C MET* 5.1 4.5 - - + -
261C PHE* 3.6 11.7 - - + -
273C ILE* 3.5 31.2 - - + +
274C HIS* 3.9 12.8 - - - +
277C THR* 3.9 22.2 - - + +
296C THR* 5.4 6.1 - - + -
298C LEU* 5.0 17.5 - - + -
308C ILE* 2.9 34.0 + - + +
309C ALA* 3.6 6.3 - - - +
311C ARG* 1.3 75.1 - - - +
313C GLN* 1.3 58.0 + - - +
315C GLU* 3.9 3.3 - - - +
316C ILE* 2.9 52.4 + - + +
328C ILE* 3.7 13.2 - - + -
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Residues in contact with GLN 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C ALA* 2.9 15.6 + - - +
310C ASP* 3.2 16.5 + - - +
312C MET* 1.3 76.6 - - - +
314C LYS* 1.3 59.8 + - - +
316C ILE* 5.0 0.4 - - - -
317C THR* 2.6 39.7 + - - +
326C ILE* 3.5 26.3 + - - +
327C LYS* 4.9 3.2 - - - +
328C ILE* 3.3 24.2 + - + +
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Residues in contact with LYS 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU* 3.0 31.4 - - + +
221C ASP* 4.4 8.3 + - - +
310C ASP 2.9 12.0 + - - +
311C ARG* 3.2 49.3 + - - +
313C GLN* 1.3 76.3 - - - +
315C GLU* 1.3 74.3 + - - +
317C THR* 3.8 4.3 - - - -
318C ALA* 2.9 30.4 + - - +
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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
----------------------------------------------------------
261C PHE* 3.0 24.0 - - - -
274C HIS* 2.9 47.3 + - + +
311C ARG* 2.8 55.7 + - - +
312C MET* 3.9 2.6 - - - +
314C LYS* 1.3 93.4 - - - +
316C ILE* 1.3 66.1 + - - +
318C ALA* 3.1 7.3 + - - +
319C LEU* 2.9 29.8 + - + +
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Residues in contact with ILE 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C HIS* 4.1 19.3 - - + +
277C THR* 3.9 25.8 - - + -
278C PHE* 3.9 16.1 - - + -
281C ILE* 5.9 1.6 - - + -
293C TYR* 4.2 18.8 - - + -
296C THR* 5.2 8.5 - - + +
312C MET* 2.9 42.4 + - + +
313C GLN 4.4 0.9 - - - +
315C GLU* 1.3 72.6 - - - +
317C THR* 1.3 59.0 + - - +
319C LEU* 3.1 2.9 + - - +
320C ALA* 2.8 32.9 + - - +
326C ILE* 3.6 26.9 - - + -
328C ILE* 5.0 7.2 - - + -
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Residues in contact with THR 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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313C GLN* 2.6 30.5 + - - +
314C LYS* 3.8 4.9 - - - -
316C ILE* 1.3 77.9 - - - +
318C ALA* 1.3 64.6 + - - +
320C ALA* 3.4 15.7 - - - +
321C PRO 5.1 0.3 - - - -
322C SER* 4.9 17.3 + - - -
324C MET 6.0 0.4 - - - +
326C ILE* 3.9 26.8 + - + +
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Residues in contact with ALA 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C LYS 2.9 19.8 + - - +
315C GLU* 3.4 7.9 - - - +
316C ILE 3.1 0.4 - - - -
317C THR* 1.3 79.9 - - - +
319C LEU* 1.3 66.1 + - + +
320C ALA 4.0 2.8 - - - +
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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
----------------------------------------------------------
274C HIS* 4.0 26.2 - - + +
275C GLU* 4.3 16.4 - - + +
278C PHE* 3.3 39.0 - - + -
315C GLU* 2.9 16.2 + - - +
316C ILE* 5.2 0.4 - - - -
318C ALA* 1.3 82.8 - - + +
320C ALA* 1.3 61.5 + - - +
321C PRO* 4.7 0.3 - - - +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C PHE* 3.4 15.3 - - + -
293C TYR* 3.7 21.5 - - + -
316C ILE 2.8 21.7 + - - +
317C THR* 3.4 10.7 - - - +
318C ALA 3.5 3.1 - - - +
319C LEU* 1.3 76.7 - - - +
321C PRO* 1.3 84.0 - - + +
322C SER* 3.2 3.6 + - - -
324C MET* 6.0 0.2 - - + -
326C ILE* 4.5 6.1 - - + -
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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