Contacts of the helix formed by residues 309 - 324 (chain A) in PDB entry 6TXC
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LEU* 6.4 0.7 - - - -
299A GLU 4.6 0.4 - - - -
300A ILE 3.4 15.0 - - - +
301A VAL 3.6 15.3 - - - +
302A SER* 3.8 3.7 + - - -
303A ASN* 3.3 25.7 + - + +
307A GLY* 3.1 16.1 + - - +
308A ILE* 1.3 73.5 - - - +
310A VAL* 1.3 64.1 + - - +
311A ASP* 3.3 9.3 - - - +
312A LYS* 3.2 38.8 + - - +
313A TRP* 3.3 24.6 - - - +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 3.7 20.5 - - + +
174A LEU* 3.8 32.0 - - + +
175A ALA* 3.7 23.8 - - + +
178A LEU* 4.0 13.9 - - + -
300A ILE* 3.0 24.1 + - + +
301A VAL* 4.2 4.0 - - - -
309A ASP* 1.3 69.8 - - - +
311A ASP* 1.3 67.2 + - - +
312A LYS 3.3 0.2 - - - -
313A TRP* 3.7 32.7 - - + +
314A ASP* 3.1 21.0 + - - +
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A HIS* 2.8 23.9 + - - -
171A VAL* 3.8 10.8 - - + -
206A HIS* 2.7 37.9 + - + +
207A ASP* 4.1 1.2 - - - +
301A VAL 3.8 14.2 + - - +
309A ASP* 3.3 11.8 - - - +
310A VAL* 1.3 82.9 - - - +
312A LYS* 1.3 64.8 + - - +
314A ASP 3.3 0.3 + - - -
315A TYR* 3.2 29.9 + - - -
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLY* 2.8 36.8 + - - +
309A ASP* 3.2 25.7 + - - +
310A VAL 3.3 0.2 - - - -
311A ASP* 1.3 78.2 - - - +
313A TRP* 1.3 63.5 + - + +
315A TYR* 3.2 27.6 + - + +
316A PHE* 2.9 47.1 + - + -
362A MET* 3.7 18.4 - - + -
363A PHE* 4.4 10.8 - - - -
366A ARG* 3.8 30.1 - - - +
508A GLY* 6.1 2.8 - - - -
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Residues in contact with TRP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A HIS* 5.4 0.2 - - - -
174A LEU* 3.9 10.8 - - + +
178A LEU* 4.0 15.9 - - + -
308A ILE* 3.9 14.7 - - + +
309A ASP* 3.3 19.9 + - - +
310A VAL* 3.3 30.5 + - + +
311A ASP 3.2 0.6 - - - -
312A LYS* 1.3 80.0 - - + +
314A ASP* 1.3 63.4 + - - +
316A PHE* 4.0 7.1 - + - +
317A ALA* 3.6 19.4 + - - +
327A ASN* 5.3 0.5 + - - -
329A PHE* 3.5 27.2 - + - -
331A TYR* 3.7 38.2 - + + -
334A PHE* 3.3 43.3 - + + -
335A ILE* 3.8 24.7 - - + -
362A MET* 3.8 19.0 - - - -
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Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 4.8 0.3 - - - +
123A HIS* 2.7 29.5 + - - -
167A HIS* 2.7 35.8 + - - -
170A GLY* 3.6 3.0 - - - -
171A VAL* 3.9 10.3 - - + +
174A LEU* 3.7 12.5 - - + +
310A VAL 3.1 15.4 + - - +
311A ASP 3.9 3.8 - - - +
313A TRP* 1.3 78.9 - - - +
315A TYR* 1.3 58.7 + - - +
317A ALA* 3.3 3.7 + - - +
318A ARG* 2.8 56.9 + - - +
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Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLN* 4.0 10.3 - - - +
164A ARG* 6.3 0.2 - - - -
167A HIS* 3.9 14.8 - + + -
311A ASP* 3.2 30.0 + - - -
312A LYS* 3.2 22.7 + - + +
314A ASP* 1.3 77.8 - - - +
316A PHE* 1.3 85.1 + + - +
318A ARG* 4.3 2.0 - - - +
319A ASP* 2.8 47.8 + - - +
366A ARG* 3.4 32.5 + - + +
370A HIS* 4.7 5.0 + - - -
374A TYR* 3.4 33.0 - + - -
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LYS* 2.9 36.5 + - + +
313A TRP* 4.0 4.5 - - - +
315A TYR* 1.3 111.4 - + - +
317A ALA* 1.3 63.8 + - - +
319A ASP* 4.5 0.3 - - - +
320A CYS* 3.1 27.9 + - - +
327A ASN* 3.7 16.6 - - - +
329A PHE* 4.0 19.7 - + + -
362A MET* 3.6 37.2 - - + -
365A THR* 4.1 13.5 - - + -
366A ARG* 3.8 32.3 - - + -
369A LEU* 4.1 13.0 - - + -
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 3.6 26.0 - - + +
123A HIS* 5.3 1.8 - - + -
313A TRP 3.6 14.0 + - - +
314A ASP* 3.3 2.6 + - - +
315A TYR 3.3 0.4 - - - -
316A PHE* 1.3 79.5 - - - +
318A ARG* 1.3 58.4 + - - +
320A CYS* 3.8 2.9 - - - +
321A HIS* 3.1 26.9 + - - +
327A ASN* 3.6 15.9 - - - +
331A TYR* 5.6 7.2 - - + -
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP* 3.0 38.6 + - - -
121A PRO* 4.6 7.3 - - - +
122A ILE* 3.5 24.6 - - + +
123A HIS* 3.8 5.9 - - - -
149A GLN* 5.4 0.4 - - - +
162A HIS* 3.9 23.1 - - + -
166A GLU* 3.4 32.5 + - - +
167A HIS* 3.6 20.2 - - - +
170A GLY* 4.1 1.6 - - - -
314A ASP* 2.8 49.0 + - - +
315A TYR* 4.2 2.9 - - - +
317A ALA* 1.3 75.6 - - - +
319A ASP* 1.3 67.4 + - - +
321A HIS* 3.2 7.6 + - - +
322A HIS* 3.1 33.7 + - - +
159B GLY* 5.9 0.6 - - - -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLN* 3.5 13.7 + - - +
150A LEU* 3.7 12.9 - - + +
162A HIS* 2.8 34.0 + - - +
315A TYR* 2.8 36.9 + - - +
316A PHE 4.5 0.4 - - - +
318A ARG* 1.3 72.4 - - - +
320A CYS* 1.3 51.4 + - - +
322A HIS* 3.3 0.7 + - - +
323A LEU* 2.7 52.3 + - + +
369A LEU* 5.6 0.4 - - + -
374A TYR* 2.7 34.4 + - + +
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Residues in contact with CYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A PHE 3.1 25.1 + - - +
317A ALA 3.8 3.8 - - - +
319A ASP* 1.3 77.6 - - - +
321A HIS* 1.3 62.5 + - - +
323A LEU* 4.4 4.5 - - - +
324A GLY* 3.1 17.2 + - - -
325A ILE* 2.9 31.9 + - - +
326A GLN* 4.0 4.0 - - - -
327A ASN* 3.6 33.0 - - + +
365A THR* 6.0 0.2 - - - -
369A LEU* 3.8 29.6 - - - -
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Residues in contact with HIS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 4.0 15.9 - - + +
122A ILE* 3.5 26.8 - - + +
317A ALA 3.1 9.1 + - - +
318A ARG 3.2 9.8 + - - +
320A CYS* 1.3 77.2 - - - +
322A HIS* 1.3 80.9 + + - +
324A GLY* 4.1 0.9 + - - -
121B PRO* 3.7 7.3 - - - +
321B HIS* 2.9 85.6 + + - -
322B HIS* 5.5 0.2 - - - -
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Residues in contact with HIS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 4.9 7.0 - - + +
122A ILE* 5.0 0.4 - - + -
159A GLY* 3.2 39.0 - - - +
160A ALA 4.4 0.4 - - - -
161A SER* 4.5 2.5 - - - -
162A HIS* 3.5 50.6 - - + +
166A GLU* 5.2 1.5 + - - -
318A ARG* 3.1 39.8 + - + +
321A HIS* 1.3 98.0 - + - +
323A LEU* 1.3 63.1 + - - +
324A GLY 3.4 0.8 + - - -
121B PRO* 3.6 7.8 - - - +
159B GLY* 4.1 10.1 + - - -
161B SER* 4.4 0.2 + - - -
321B HIS* 4.7 1.3 - - - -
322B HIS* 3.4 39.5 - + - +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.6 25.6 - - + -
153A GLY 6.2 0.2 - - - -
157A PHE* 3.4 57.9 - - + +
159A GLY 5.5 0.2 + - - -
160A ALA* 4.2 3.8 - - + -
162A HIS* 5.4 0.4 - - + -
319A ASP* 2.7 44.0 + - + +
320A CYS* 4.1 3.4 - - - +
322A HIS* 1.3 75.1 - - - +
324A GLY* 1.3 57.7 + - - +
325A ILE* 4.2 20.0 - - + +
369A LEU* 4.5 7.0 - - + -
373A ALA* 3.7 24.0 - - + -
374A TYR* 4.3 4.9 - - + -
119B ASN* 3.8 14.4 + - - +
121B PRO* 4.7 1.2 - - - -
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Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A CYS 3.1 6.3 + - - -
321A HIS 4.1 1.9 + - - -
322A HIS 3.4 2.8 + - - -
323A LEU* 1.3 78.4 - - - +
325A ILE* 1.3 62.5 + - - +
119B ASN* 3.3 22.4 + - - +
121B PRO* 4.1 22.0 - - - -
125B HIS* 5.2 2.1 - - - -
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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