Contacts of the helix formed by residues 310 - 321 (chain A) in PDB entry 1XTG
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 LEU 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A LEU* 3.9 17.3 - - + -
300A ALA* 4.1 9.0 - - + +
301A LYS* 3.2 34.5 - - - +
302A SER* 3.9 15.3 - - - +
303A ILE* 4.1 23.5 - - + +
309A SER* 1.3 73.4 - - - +
311A GLN* 1.3 64.9 + - - +
313A MET* 3.3 1.9 + - - +
314A LYS* 3.0 48.3 + - + +
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Residues in contact with GLN 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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309A SER* 3.3 7.2 + - - +
310A LEU* 1.3 82.3 - - - +
312A TYR* 1.3 57.8 + - - +
314A LYS* 3.4 8.5 + - + +
315A ASN* 3.0 29.3 + - + +
325A GLU* 5.8 1.8 + - - -
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Residues in contact with TYR 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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308A ALA* 3.9 9.9 - - + -
309A SER* 3.2 22.3 + - - +
311A GLN* 1.3 80.6 - - - +
313A MET* 1.3 69.5 + - - +
315A ASN* 3.1 12.4 + - + +
316A VAL* 3.0 38.8 + - + +
172B ASP* 2.9 42.4 + - - -
173B THR 3.6 0.4 + - - -
174B GLN* 3.4 57.6 + - + +
176B ARG* 3.7 15.0 - - + -
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Residues in contact with MET 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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115A ILE* 6.4 0.4 - - + -
118A TRP* 3.4 50.5 - - + +
127A LEU* 4.7 7.4 - - + -
303A ILE* 3.4 30.1 - - + -
306A THR* 4.3 1.3 - - + -
308A ALA* 4.1 9.6 - - + -
309A SER 3.1 12.2 + - - +
310A LEU 3.9 2.7 - - - +
312A TYR* 1.3 86.5 - - - +
314A LYS* 1.3 65.3 + - - +
316A VAL* 3.4 13.8 + - + +
317A PHE* 3.2 33.2 - - + -
176B ARG* 3.7 35.0 - - - +
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Residues in contact with LYS 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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127A LEU* 4.1 8.1 - - + -
297A LEU* 3.0 38.7 + - + +
298A ASN* 4.5 5.1 + - - +
300A ALA* 2.6 39.4 + - - +
310A LEU* 3.0 40.4 + - + +
311A GLN* 3.7 8.3 - - - +
313A MET* 1.3 76.8 - - - +
315A ASN* 1.3 58.2 + - - +
317A PHE* 3.4 4.5 + - - +
318A LYS* 3.0 25.1 + - - +
331A PHE* 3.8 26.2 - - + -
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Residues in contact with ASN 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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311A GLN* 3.0 16.4 + - + +
312A TYR* 3.1 15.3 + - + +
314A LYS* 1.3 76.0 - - - +
316A VAL* 1.3 66.8 + - - +
318A LYS* 3.5 30.1 - - - +
319A GLU* 3.0 43.7 + - - +
325A GLU* 4.6 4.6 + - - -
331A PHE* 4.6 3.3 - - + -
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Residues in contact with VAL 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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115A ILE* 3.8 29.4 - - + -
312A TYR* 3.0 44.0 + - + +
313A MET* 3.6 15.5 - - + +
314A LYS 3.3 0.6 - - - -
315A ASN* 1.3 77.7 + - - +
317A PHE* 1.3 77.1 + - + +
319A GLU* 3.3 11.4 + - - +
320A LYS* 2.9 22.8 + - + +
171B ILE* 3.5 8.7 - - + +
172B ASP* 3.9 21.3 - - + +
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Residues in contact with PHE 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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115A ILE* 3.4 36.3 - - + -
116A PRO 3.6 7.4 - - - -
117A PHE* 3.6 27.1 - + + -
118A TRP* 3.5 45.5 - + + -
127A LEU* 5.4 2.0 - - + -
297A LEU* 3.9 25.6 - - + -
313A MET* 3.2 31.4 - - + -
314A LYS 3.4 3.0 + - - +
315A ASN 3.2 0.2 - - - -
316A VAL* 1.3 79.9 - - + +
318A LYS* 1.3 66.2 + - - +
319A GLU 3.1 1.8 - - - -
320A LYS* 4.0 6.5 - - + -
321A TYR* 3.0 47.0 + + + +
323A LEU* 4.3 0.7 - - - +
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Residues in contact with LYS 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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297A LEU* 4.7 0.8 - - - +
314A LYS 3.0 14.8 + - - +
315A ASN* 3.2 28.1 + - - +
317A PHE* 1.3 75.4 - - - +
319A GLU* 1.3 62.5 + - + +
322A LEU* 3.1 6.8 + - - -
323A LEU* 2.8 64.6 + - + +
325A GLU* 3.2 38.3 + - - +
331A PHE* 3.8 23.1 - - + -
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Residues in contact with GLU 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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113A ARG* 3.2 21.8 + - - +
315A ASN* 3.0 39.2 + - - +
316A VAL* 3.5 9.3 - - - +
318A LYS* 1.3 81.0 - - + +
320A LYS* 1.3 64.6 + - - +
322A LEU* 3.3 16.2 + - - +
171B ILE* 3.0 36.3 - - + +
172B ASP 4.8 1.4 + - - -
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Residues in contact with LYS 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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113A ARG* 3.7 17.2 - - - +
114A GLY* 3.8 10.3 - - - -
115A ILE 2.6 36.3 + - - +
180A TYR 3.0 9.5 + - - -
232A LEU 3.0 27.8 + - - -
233A TYR* 3.5 31.8 + - + +
316A VAL* 2.9 18.0 + - + +
317A PHE* 3.3 12.1 + - + +
319A GLU* 1.3 79.0 - - - +
321A TYR* 1.3 100.9 + - + +
322A LEU 3.5 0.3 + - - -
341A LEU* 4.2 5.5 - - - +
167B MET* 4.5 5.5 - - - +
171B ILE* 3.8 7.6 - - + +
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Residues in contact with TYR 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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117A PHE* 3.8 7.9 - + - +
179A GLY 2.7 29.5 + - - -
180A TYR 3.3 5.5 + - - -
233A TYR* 4.4 4.5 - + - -
290A PHE* 3.6 43.4 - + + -
293A ILE* 3.7 34.4 - - + +
317A PHE* 3.0 41.1 + + + +
320A LYS* 1.3 116.1 + - + +
322A LEU* 1.3 71.8 + - - +
323A LEU* 3.2 24.1 + - + +
333A VAL* 5.8 1.6 - - - +
338A PHE* 5.9 2.4 - - - -
341A LEU* 4.2 7.6 - - - +
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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