Contacts of the helix formed by residues 318 - 333 (chain A) in PDB entry 2XT6
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 GLN 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A TYR* 4.3 0.2 - - - -
317A ILE* 1.4 76.1 - - - +
319A GLY* 1.3 61.9 + - - +
320A ALA* 3.4 31.9 - - - +
321A GLU* 2.9 35.4 + - + +
322A SER 3.0 10.9 + - - -
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 4.9 4.3 - - - -
312A TYR* 3.3 29.7 + - - -
317A ILE 4.1 0.2 + - - -
318A GLN* 1.3 74.3 - - - +
320A ALA* 1.3 60.3 + - - +
322A SER* 3.9 4.0 - - - -
323A GLY* 3.3 19.1 + - - -
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Residues in contact with ALA 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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318A GLN* 3.1 31.0 - - - +
319A GLY* 1.3 76.8 - - - +
321A GLU* 1.4 60.7 + - - +
323A GLY* 3.6 2.1 + - - -
324A ASP* 3.1 31.1 + - - +
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Residues in contact with GLU 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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172A PHE* 3.7 31.8 - - + +
173A PRO* 5.1 0.3 - - - +
174A ASN* 3.3 44.9 + - - +
175A MET* 4.3 13.9 - - + -
316A ILE 5.4 0.7 - - - +
317A ILE* 4.8 4.1 - - + +
318A GLN* 2.9 28.0 + - + +
320A ALA* 1.4 74.8 - - - +
322A SER* 1.3 59.9 + - - +
324A ASP* 3.0 12.6 + - - +
325A PHE* 2.9 26.3 + - - +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 2.5 27.1 + - - -
175A MET* 3.9 13.0 - - - +
310A SER* 2.8 20.6 + - - -
312A TYR* 3.2 27.1 - - - -
317A ILE* 4.3 3.4 - - - -
318A GLN 3.0 12.6 + - - -
319A GLY 3.9 4.0 - - - -
321A GLU* 1.3 74.4 - - - +
323A GLY* 1.3 60.7 + - - +
325A PHE* 3.3 12.3 + - - +
326A LEU* 3.3 17.7 + - - +
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Residues in contact with GLY 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 4.2 9.1 + - - -
129A ARG* 3.8 8.3 + - - -
319A GLY 3.3 12.2 + - - -
320A ALA 3.9 3.6 - - - -
321A GLU 3.2 1.2 - - - -
322A SER* 1.3 74.3 - - - +
324A ASP* 1.4 62.4 + - - +
326A LEU* 3.5 8.3 + - - +
327A ARG* 2.9 27.1 + - - +
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Residues in contact with ASP 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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172A PHE* 3.5 22.6 - - + -
320A ALA* 3.1 21.4 + - - +
321A GLU* 3.0 10.4 + - - +
323A GLY* 1.4 73.6 - - - +
325A PHE* 1.4 55.6 + - - +
327A ARG* 3.5 28.4 + - - +
328A THR* 2.8 38.5 + - - -
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Residues in contact with PHE 325 (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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165A ILE* 3.8 14.6 - - + -
168A ALA* 3.5 36.1 - - + -
169A VAL* 3.5 26.0 - - + -
172A PHE* 3.9 13.4 - + + -
175A MET* 3.5 45.3 - - + -
253A ILE* 4.4 1.6 - - + -
278A ILE* 3.5 30.7 - - + -
310A SER* 5.2 0.4 - - - -
321A GLU 2.9 11.1 + - - +
322A SER 3.3 10.9 + - - +
324A ASP* 1.4 75.3 - - - +
326A LEU* 1.3 62.0 + - + +
328A THR* 3.2 4.7 + - - -
329A ILE* 3.1 47.6 + - + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 3.3 35.7 - - - +
128A VAL 4.0 0.9 - - - +
129A ARG* 3.5 25.3 - - + -
131A ILE* 3.7 4.5 - - - +
278A ILE* 4.7 4.0 - - + -
308A LEU* 3.7 43.3 - - + +
309A THR 4.1 10.8 - - - +
310A SER* 4.0 13.5 - - - -
322A SER 3.3 9.9 + - - +
323A GLY* 3.8 8.7 - - - +
324A ASP 3.3 0.2 - - - -
325A PHE* 1.3 80.0 - - + +
327A ARG* 1.4 60.2 + - - +
329A ILE* 3.4 12.2 + - + +
330A HIS* 2.9 28.2 + - - +
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Residues in contact with ARG 327 (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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129A ARG* 3.5 35.2 - - - +
172A PHE* 4.2 4.4 - - - -
323A GLY 2.9 18.8 + - - +
324A ASP* 3.1 37.8 + - - +
326A LEU* 1.4 75.3 - - - +
328A THR* 1.3 68.1 + - - +
330A HIS* 3.2 4.5 - - + +
331A GLN* 3.0 75.3 + - + +
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Residues in contact with THR 328 (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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168A ALA* 3.8 26.9 - - + -
171A LYS* 4.8 7.4 - - + +
172A PHE* 3.2 23.6 - - + -
324A ASP 2.8 17.7 + - - -
325A PHE 3.5 4.7 - - - -
327A ARG* 1.3 84.0 + - - +
329A ILE* 1.4 57.7 + - - +
331A GLN* 3.4 15.9 + - - +
332A LEU* 2.9 35.6 + - + +
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Residues in contact with ILE 329 (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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131A ILE* 4.3 0.7 - - + -
161A LEU* 3.8 16.8 - - + -
164A ALA* 4.3 7.0 - - + +
165A ILE* 3.8 25.8 - - + +
168A ALA* 3.7 14.6 - - + -
278A ILE* 5.0 1.1 - - + -
308A LEU* 3.6 26.0 - - + -
325A PHE* 3.1 47.9 + - + +
326A LEU* 3.4 16.8 + - + +
328A THR* 1.4 72.0 - - - +
330A HIS* 1.3 64.9 + - - +
332A LEU* 3.8 6.0 - - - +
333A LEU* 3.0 33.5 + - + +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 3.3 28.6 + - - +
130A ALA 4.1 5.9 + - - -
131A ILE* 3.6 32.5 - - + +
132A PRO* 3.3 27.8 - - + +
326A LEU 2.9 14.6 + - - +
327A ARG* 3.2 12.8 + - + +
329A ILE* 1.3 77.9 - - - +
331A GLN* 1.3 65.2 + - - +
333A LEU* 3.4 8.0 + - - +
334A LEU* 3.5 30.4 + - + +
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Residues in contact with GLN 331 (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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327A ARG* 3.0 49.8 + - + +
328A THR* 3.6 19.7 + - - +
329A ILE 3.4 0.2 - - - -
330A HIS* 1.3 79.4 + - - +
332A LEU* 1.4 56.5 + - + +
334A LEU* 3.3 7.4 + - - +
335A ASP* 3.0 28.3 + - - +
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Residues in contact with LEU 332 (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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164A ALA* 3.3 38.4 - - + +
167A GLN* 3.7 20.2 - - + -
168A ALA* 4.1 11.7 - - + +
328A THR* 2.9 28.0 + - + +
329A ILE* 3.8 6.1 - - - +
330A HIS 3.4 0.2 - - - -
331A GLN* 1.4 66.1 - - + +
333A LEU* 1.4 58.5 + - - +
334A LEU 3.0 10.2 + - - -
335A ASP* 3.0 26.2 + - + +
338A PHE* 3.3 40.9 - - + +
339A PHE* 4.2 0.2 - - - -
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 4.6 12.6 - - + -
132A PRO 4.6 2.5 - - - +
135A LEU* 3.9 6.1 - - - +
136A MET* 4.1 42.8 + - + +
160A LEU* 4.1 15.7 - - + +
161A LEU* 3.9 15.7 - - + -
164A ALA* 4.4 5.8 - - + -
306A ILE* 4.5 10.1 - - + -
308A LEU* 5.4 0.2 - - + -
329A ILE* 3.0 36.1 + - + +
330A HIS 3.4 2.7 + - - +
332A LEU* 1.4 72.9 - - - +
334A LEU* 1.3 68.8 + - + +
338A PHE* 3.9 22.0 - - + -
339A PHE* 3.5 20.2 - - + -
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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
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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