Contacts of the helix formed by residues 309 - 324 (chain C) in PDB entry 6TXA
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 ASP 309 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C LEU* 6.4 0.7 - - - -
299C GLU 4.5 0.4 - - - -
300C ILE 3.4 14.1 - - - +
301C VAL 3.5 15.3 - - - +
302C SER* 3.8 3.2 + - - -
303C ASN* 3.3 24.5 + - + +
307C GLY* 3.1 18.4 + - - +
308C ILE* 1.3 75.1 - - - +
310C VAL* 1.3 65.5 + - - +
311C ASP* 3.3 9.6 - - - +
312C LYS* 3.2 38.0 + - - +
313C TRP* 3.3 25.1 - - - +
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Residues in contact with VAL 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C VAL* 3.7 33.2 - - + +
174C LEU* 3.7 27.9 - - + +
175C ALA* 3.7 12.8 - - + +
178C LEU* 4.1 12.6 - - + -
300C ILE* 3.0 24.1 + - + +
301C VAL* 4.3 3.4 - - - -
309C ASP* 1.3 70.3 - - - +
311C ASP* 1.3 67.2 + - - +
313C TRP* 3.6 33.0 - - + +
314C ASP* 3.1 24.6 + - - +
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Residues in contact with ASP 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ARG* 5.7 0.2 + - - -
167C HIS* 2.6 26.7 + - - -
171C VAL* 3.8 8.9 - - + +
206C HIS* 2.5 38.1 + - + +
207C ASP* 3.7 4.5 - - - +
233C HIS* 5.4 3.3 + - - -
301C VAL 3.8 13.2 + - - +
302C SER* 6.1 0.4 - - - -
309C ASP* 3.3 11.8 + - - +
310C VAL* 1.3 80.9 - - - +
312C LYS* 1.3 64.2 + - + +
314C ASP 3.4 0.2 + - - -
315C TYR* 3.1 34.0 + - - -
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Residues in contact with LYS 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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307C GLY* 2.7 36.2 + - - +
309C ASP* 3.2 24.9 + - - +
310C VAL 3.2 0.4 - - - -
311C ASP* 1.3 79.5 - - - +
313C TRP* 1.3 67.8 + - + +
314C ASP 3.3 0.2 + - - -
315C TYR* 3.3 26.8 + - + +
316C PHE* 3.0 41.0 + - + -
362C MET* 3.6 19.3 - - + -
363C PHE* 4.4 10.1 - - - -
366C ARG* 3.7 31.8 - - - +
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Residues in contact with TRP 313 (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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174C LEU* 3.9 11.0 - - + -
178C LEU* 4.0 17.3 - - + -
308C ILE* 4.0 12.9 - - + +
309C ASP* 3.3 19.7 + - - -
310C VAL* 3.2 31.9 + - + +
312C LYS* 1.3 79.2 - - + +
314C ASP* 1.3 64.5 + - - +
316C PHE* 3.7 7.5 + + - +
317C ALA* 3.4 19.4 + - - +
327C ASN* 5.3 0.5 + - - -
329C PHE* 3.4 29.7 - + - -
331C TYR* 3.7 36.9 - + + -
334C PHE* 3.3 43.3 - + + -
335C ILE* 3.7 25.6 - - + -
362C MET* 3.8 16.6 - - + -
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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
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122C ILE* 5.1 0.2 - - - +
123C HIS* 2.7 30.1 + - - -
167C HIS* 2.8 30.6 + - - -
170C GLY* 3.4 5.0 - - - -
171C VAL* 3.8 11.0 - - + +
174C LEU* 3.7 12.9 - - + +
310C VAL 3.1 15.4 + - - +
311C ASP 3.8 3.4 - - - +
313C TRP* 1.3 77.7 - - - +
315C TYR* 1.3 58.9 + - - +
317C ALA* 3.2 4.2 + - - +
318C ARG* 2.8 58.5 + - - +
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Residues in contact with TYR 315 (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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149C GLN* 3.9 19.5 - - - +
164C ARG* 6.4 0.4 - - - -
167C HIS* 4.0 4.3 - + + -
311C ASP* 3.1 34.8 + - - +
312C LYS* 3.6 20.8 - - + +
314C ASP* 1.3 80.7 - - - +
316C PHE* 1.3 85.5 + + - +
318C ARG* 4.2 4.7 - - - -
319C ASP* 2.8 45.0 + - - +
366C ARG* 3.5 32.4 + - - +
370C HIS* 4.9 4.8 + - - -
374C TYR* 3.3 34.1 - + - -
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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
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312C LYS* 3.0 37.6 + - + +
313C TRP* 3.9 5.2 - - - +
315C TYR* 1.3 113.9 - + - +
317C ALA* 1.3 64.2 + - - +
319C ASP* 4.4 0.2 - - - +
320C CYS* 3.1 26.7 + - - +
327C ASN* 3.9 16.6 - - - +
329C PHE* 4.2 19.1 - + + -
362C MET* 3.6 34.5 - - + -
365C THR* 4.1 12.8 - - + -
366C ARG* 3.8 33.9 - - + -
369C LEU* 3.9 17.0 - - + -
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Residues in contact with ALA 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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122C ILE* 3.6 25.0 - - + +
123C HIS* 5.1 2.7 - - + -
313C TRP 3.4 9.3 + - - +
314C ASP* 3.2 9.1 + - - +
316C PHE* 1.3 79.6 - - - +
318C ARG* 1.3 61.6 + - - +
320C CYS* 3.9 1.7 - - - +
321C HIS* 3.2 23.6 + - - +
327C ASN* 3.7 16.8 - - - +
331C TYR* 5.1 9.2 - - + -
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Residues in contact with ARG 318 (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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120C ASP* 2.8 41.8 + - - -
121C PRO* 4.7 5.3 - - - +
122C ILE* 3.5 23.7 - - + +
123C HIS* 3.7 4.8 - - - -
149C GLN* 5.1 1.3 - - - +
162C HIS* 3.7 24.2 - - + -
166C GLU* 3.4 32.6 + - - +
167C HIS* 3.6 20.2 - - - +
170C GLY* 4.0 1.0 - - - -
314C ASP* 2.8 53.8 + - - +
315C TYR* 4.2 3.6 - - - +
317C ALA* 1.3 73.2 - - - +
319C ASP* 1.3 67.1 + - - +
321C HIS* 3.2 1.9 + - - +
322C HIS* 3.1 38.9 + - + +
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Residues in contact with ASP 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C GLN* 3.5 13.9 + - - +
150C LEU* 3.6 14.3 - - + +
162C HIS* 2.8 33.7 + - - +
315C TYR* 2.8 38.0 + - - +
316C PHE 4.4 0.4 - - - +
318C ARG* 1.3 72.8 - - - +
320C CYS* 1.3 53.4 + - - +
322C HIS* 3.2 2.1 + - - +
323C LEU* 2.6 52.9 + - + +
369C LEU* 5.5 1.1 - - + -
374C TYR* 2.6 34.0 + - + +
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Residues in contact with CYS 320 (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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316C PHE 3.1 25.1 + - - +
317C ALA 3.9 3.8 - - - +
319C ASP* 1.3 77.9 - - - +
321C HIS* 1.3 63.0 + - - +
323C LEU* 4.4 4.7 - - - -
324C GLY* 3.1 16.8 + - - -
325C ILE* 3.0 33.1 + - - +
326C GLN 4.0 4.0 - - - -
327C ASN* 3.6 32.5 - - + +
365C THR* 6.0 0.9 - - - -
369C LEU* 3.8 28.7 - - - -
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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
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121C PRO* 4.2 23.1 + - + +
122C ILE* 3.5 19.1 - - + +
317C ALA 3.2 13.0 + - - +
318C ARG 3.2 9.4 + - - +
320C CYS* 1.3 80.9 - - - +
322C HIS* 1.3 86.0 + + - +
324C GLY* 4.1 4.2 + - - -
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Residues in contact with HIS 322 (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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121C PRO* 4.9 8.1 - - + +
122C ILE* 4.9 1.6 - - + -
159C GLY* 3.2 44.8 - - - +
160C ALA 4.4 0.4 - - - -
161C SER* 4.5 6.7 - - - -
162C HIS* 3.6 49.1 - - + +
166C GLU* 5.3 3.2 + - + -
318C ARG* 3.1 38.3 + - + +
319C ASP 3.2 2.0 + - - -
321C HIS* 1.3 100.3 + + - +
323C LEU* 1.3 63.6 + - - +
324C GLY 3.3 0.9 - - - -
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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
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150C LEU* 3.7 24.5 - - + -
153C GLY* 6.2 0.4 - - - -
157C PHE* 3.4 60.5 - - + +
158C PRO* 6.0 0.3 - - - +
159C GLY* 5.2 2.4 + - - -
160C ALA* 4.3 3.8 - - + -
319C ASP* 2.6 44.1 + - + +
320C CYS* 4.1 2.5 - - - +
322C HIS* 1.3 74.2 - - - +
324C GLY* 1.3 60.1 + - - +
325C ILE* 4.1 18.2 - - + +
369C LEU* 4.3 11.4 - - + -
373C ALA* 3.7 24.2 - - + -
374C TYR* 4.6 2.2 - - + -
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Residues in contact with GLY 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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330B ASP* 4.8 9.0 - - - +
320C CYS 3.1 7.6 + - - -
321C HIS 4.1 4.2 + - - -
322C HIS 3.3 2.4 + - - -
323C LEU* 1.3 79.4 - - - +
325C ILE* 1.3 65.2 + - - +
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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