Contacts of the helix formed by residues 305 - 318 (chain C) in PDB entry 1M6X
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 HIS 305 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191C ARG* 4.2 24.6 - - + +
192C PHE 5.5 0.2 + - - -
302C PRO* 4.1 6.1 - - + -
303C LYS 3.0 0.2 - - - -
304C SER* 1.3 79.0 + - - +
306C ILE* 1.3 63.5 + - - +
307C GLY 3.1 3.7 + - - -
308C ARG* 3.2 29.0 + - + +
309C HIS* 2.8 42.1 + + + -
13G C 4.7 11.2 + - - -
14G T 3.8 19.2 + - - -
24I T 2.8 54.4 + - - -
25I A 3.2 9.2 + - - +
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Residues in contact with ILE 306 (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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144C LEU* 4.9 8.3 - - + -
147C LEU* 4.3 21.5 - - + -
161C ILE* 4.6 2.2 - - + -
182C PHE* 3.8 24.5 - - + -
283C TYR* 5.0 0.2 - - - +
287C LEU* 4.5 4.0 - - + -
295C ILE* 5.0 4.7 - - + -
296C PHE* 3.7 33.9 - - + -
302C PRO* 4.1 20.2 - - + +
303C LYS 3.0 19.6 + - - +
304C SER* 4.3 2.7 - - - +
305C HIS* 1.3 78.9 - - - +
307C GLY* 1.3 75.2 + - - +
309C HIS* 3.2 9.4 + - + +
310C LEU* 2.9 39.5 + - + +
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Residues in contact with GLY 307 (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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182C PHE* 4.4 4.9 - - - -
185C THR* 3.7 20.9 - - - -
186C PHE* 3.6 20.6 - - - -
304C SER 3.6 3.0 + - - -
305C HIS 3.1 1.2 - - - -
306C ILE* 1.3 87.7 - - - +
308C ARG* 1.3 62.6 + - - +
310C LEU* 3.3 11.0 + - - +
311C MET* 3.2 17.2 + - - +
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Residues in contact with ARG 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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185C THR* 4.3 2.8 + - - -
189C CYS* 3.3 42.6 + - - +
190C GLY* 4.3 9.8 + - - +
191C ARG* 2.9 60.6 - - - +
194C ASP* 5.0 2.0 + - - -
304C SER 4.9 0.4 + - - -
305C HIS* 3.2 24.5 + - + +
307C GLY* 1.3 71.5 - - - +
309C HIS* 1.3 68.2 + - + +
311C MET* 3.0 5.0 + - - +
312C THR* 2.8 28.4 + - - +
328C GLY 3.0 23.0 + - - -
329C ASN 3.8 2.8 + - - -
330C TRP* 3.5 30.0 - - + +
14G T 3.0 22.0 + - - -
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Residues in contact with HIS 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 4.0 31.4 - - + -
302C PRO* 4.1 15.3 - - + +
305C HIS* 2.8 50.1 + + + -
306C ILE* 3.2 14.0 + - + +
308C ARG* 1.3 79.3 - - + +
310C LEU* 1.3 65.6 + - - +
312C THR* 3.1 10.4 + - - -
313C SER* 2.9 27.7 + - - -
13G C 5.2 8.4 + - - -
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 5.5 0.9 - - + -
147C LEU* 4.8 9.2 - - + -
148C LEU* 4.3 12.6 - - + -
154C ILE* 4.0 27.8 - - + +
157C ILE* 4.4 17.9 - - + -
158C THR* 4.7 7.9 - - - +
161C ILE* 4.3 6.7 - - + -
182C PHE* 4.0 29.6 - - + -
186C PHE* 3.8 15.5 - - + -
306C ILE* 2.9 34.0 + - + +
307C GLY* 3.5 7.6 - - - +
308C ARG 3.2 0.2 - - - -
309C HIS* 1.3 76.5 - - - +
311C MET* 1.3 52.4 + - - +
313C SER* 3.2 6.8 + - - -
314C PHE* 2.7 33.8 + - - +
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Residues in contact with MET 311 (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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186C PHE* 3.3 59.2 - - + +
187C ILE 4.1 0.4 - - - +
189C CYS* 3.7 20.2 - - + -
307C GLY 3.2 3.7 + - - +
308C ARG 3.0 7.4 + - - +
310C LEU* 1.3 75.8 - - - +
312C THR* 1.3 67.3 + - - +
314C PHE* 3.4 24.1 - - + +
315C LEU* 2.9 39.0 + - + +
354C TYR* 3.3 30.5 - - + +
358C VAL* 3.8 23.1 - - + -
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Residues in contact with THR 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C CYS* 3.9 13.8 - - - -
308C ARG* 2.8 20.3 + - - +
309C HIS* 3.3 12.3 - - - -
311C MET* 1.3 75.4 - - - +
313C SER* 1.3 64.4 + - - +
315C LEU* 3.7 6.6 + - - +
316C SER* 3.2 22.3 + - - -
324C THR* 4.4 22.3 + - + +
330C TRP* 3.9 13.4 - - + -
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Residues in contact with SER 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 5.0 4.3 - - - +
148C LEU* 3.5 36.4 - - - +
154C ILE* 4.5 4.0 - - - -
309C HIS* 2.9 14.3 + - - +
310C LEU 3.5 7.6 - - - -
312C THR* 1.3 77.0 - - - +
314C PHE* 1.3 57.7 + - - +
316C SER* 3.1 6.4 + - - -
317C MET* 2.7 39.9 + - - +
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Residues in contact with PHE 314 (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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154C ILE* 4.2 32.5 - - + +
155C TRP* 4.5 25.1 - + - -
186C PHE* 4.7 2.5 - + + -
310C LEU 2.7 18.4 + - - +
311C MET* 3.4 33.9 - - + +
313C SER* 1.3 73.2 - - - +
315C LEU* 1.3 57.4 + - + +
317C MET* 3.7 7.1 - - - +
318C LYS* 2.7 63.7 + - + +
357C LEU* 3.4 42.2 - - + -
358C VAL* 4.4 14.1 - - + -
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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
----------------------------------------------------------
189C CYS* 5.8 1.8 - - - -
311C MET* 2.9 31.4 + - + +
312C THR* 3.9 2.9 - - - +
314C PHE* 1.3 87.3 - - + +
316C SER* 1.3 58.7 + - - +
318C LYS* 3.4 3.1 + - - -
319C GLY 3.0 4.5 + - - -
320C LEU* 2.7 57.9 + - + +
323C LEU* 4.4 4.9 - - + -
324C THR* 3.8 39.5 - - + +
327C VAL* 4.3 9.2 - - + -
354C TYR* 3.9 35.0 - - + -
357C LEU* 5.0 2.0 - - + -
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Residues in contact with SER 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C THR* 3.2 12.9 + - - -
313C SER* 3.1 10.6 + - - -
315C LEU* 1.3 78.4 - - - +
317C MET* 1.3 56.2 + - - +
319C GLY* 2.6 27.9 + - - -
321C THR* 3.6 26.7 - - - +
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Residues in contact with MET 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 5.6 7.9 - - + -
313C SER* 2.7 22.8 + - - +
314C PHE* 3.8 10.3 - - - +
316C SER* 1.3 75.3 + - - +
318C LYS* 1.3 90.6 + - + +
319C GLY* 3.2 1.2 + - - -
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Residues in contact with LYS 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C PHE* 2.7 57.1 + - + +
315C LEU 3.9 4.7 - - - +
317C MET* 1.3 90.0 - - + +
319C GLY* 1.3 61.3 + - - +
320C LEU* 4.4 13.2 - - + -
357C LEU* 4.3 20.2 - - + +
363C ALA* 5.2 6.7 - - - +
364C TYR* 3.6 35.9 + - + +
366C PRO* 4.6 6.6 - - - +
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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