Contacts of the helix formed by residues 293 - 310 (chain A) in PDB entry 1SXG
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 PRO 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 4.0 10.5 - - + -
291A VAL* 3.5 19.1 - - + +
292A GLN* 1.4 79.0 - - - -
294A MET* 1.3 63.2 + - - +
295A TYR 3.3 2.0 - - - -
296A ASP* 3.2 32.2 + - + +
297A ILE* 2.9 30.9 + - + +
321A LEU* 4.8 2.2 - - + -
322A PRO 3.6 22.9 - - - +
323A HIS* 4.7 1.1 - - - -
324A ARG* 4.2 19.1 - - - +
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 3.9 24.9 - - + -
77A GLU* 3.3 53.2 - - + +
78A LEU* 3.5 29.5 - - + +
81A GLY* 4.9 6.5 - - - -
275A ASP 5.0 6.1 - - - +
276A ASN 5.2 5.8 - - - +
277A THR* 5.4 0.7 - - - -
292A GLN 2.8 12.8 + - - +
293A PRO* 1.3 71.8 - - - +
295A TYR* 1.3 68.3 + - + +
297A ILE* 3.5 5.8 + - - -
298A GLY* 2.9 22.5 + - - -
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Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY* 4.1 22.5 - - - -
84A ASP* 3.8 37.7 + - + -
85A ILE* 4.2 18.9 - - + +
293A PRO 3.3 0.6 - - - -
294A MET* 1.3 85.6 - - + +
296A ASP* 1.3 64.6 + - - +
298A GLY* 4.3 1.3 - - - +
299A ALA* 2.8 32.1 + - - +
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 3.2 30.8 + - + +
295A TYR* 1.3 78.9 - - - +
297A ILE* 1.3 64.1 + - - +
299A ALA* 3.7 3.7 - - - +
300A VAL* 3.0 30.7 + - + +
321A LEU* 3.4 27.6 - - + +
322A PRO* 5.1 6.4 - - - +
324A ARG* 5.6 1.2 + - - -
3256A 171 4.6 16.2 + - - +
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Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 6.0 0.7 - - + -
78A LEU* 4.0 21.5 - - + -
145A ALA* 4.0 24.0 - - + -
146A ALA* 4.3 3.1 - - + +
157A VAL* 4.0 30.3 - - + +
158A THR* 4.3 20.2 - - - -
159A ILE* 4.6 10.1 - - + -
292A GLN* 4.9 10.1 - - + +
293A PRO* 2.9 26.4 + - + +
294A MET* 3.5 8.5 - - - +
296A ASP* 1.3 75.7 - - - +
298A GLY* 1.3 64.9 + - - +
301A ALA* 2.9 27.0 + - - +
321A LEU* 4.0 12.6 - - + -
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.4 0.2 - - - +
82A ILE* 3.9 29.6 - - - -
85A ILE* 4.2 9.4 - - - -
294A MET 2.9 16.2 + - - -
295A TYR* 3.7 2.9 - - - -
297A ILE* 1.3 77.2 - - - +
299A ALA* 1.3 61.5 + - - +
301A ALA* 3.7 3.4 - - - +
302A MET* 3.0 28.5 + - - +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.0 16.1 - - + +
295A TYR 2.8 20.6 + - - +
296A ASP 3.7 3.1 - - - +
298A GLY* 1.3 69.0 - - - +
300A VAL* 1.3 65.7 + - + +
302A MET* 3.0 5.0 + - - +
303A ARG* 3.0 39.0 + - - +
3256A 171 3.7 38.4 - - + +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 4.0 17.7 - - + -
296A ASP* 3.0 18.0 + - - +
299A ALA* 1.3 75.7 - - + +
301A ALA* 1.3 65.4 + - - +
302A MET 3.1 0.2 + - - -
303A ARG* 3.2 17.3 - - + +
304A LEU* 3.0 28.5 + - + +
319A VAL* 4.0 35.0 - - + -
321A LEU* 3.4 24.7 - - + -
3256A 171 5.5 3.4 - - - +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 5.6 1.1 - - + -
121A ILE* 4.5 19.2 - - + +
143A VAL* 4.2 14.0 - - + +
145A ALA* 5.0 4.3 - - + -
157A VAL* 3.6 21.5 - - + +
297A ILE 2.9 20.9 + - - +
298A GLY* 3.7 6.1 - - - +
300A VAL* 1.3 78.0 - - - +
302A MET* 1.3 57.4 + - + +
304A LEU* 3.6 4.6 - - - +
305A LEU* 2.9 31.2 + - - +
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Residues in contact with MET 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 4.1 12.8 - - + -
82A ILE* 3.3 23.3 - - + +
85A ILE* 3.7 19.7 - - + -
86A ALA* 4.2 11.4 - - + +
89A TYR* 3.8 20.0 - - + -
91A TYR* 4.1 27.6 - - - -
121A ILE* 3.3 35.4 - - + -
298A GLY 3.0 16.4 + - - +
299A ALA 3.0 8.2 + - - +
301A ALA* 1.3 73.6 - - + +
303A ARG* 1.3 62.3 + - - +
304A LEU 3.1 0.9 - - - -
305A LEU* 3.9 4.4 - - - +
306A THR* 2.7 35.9 + - - -
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.5 19.5 + - - +
299A ALA* 3.0 31.8 + - - +
300A VAL* 3.2 23.6 - - + +
302A MET* 1.3 73.5 - - - +
304A LEU* 1.3 57.5 + - + +
306A THR* 3.6 5.1 - - - -
307A LYS* 2.8 50.3 + - + +
3256A 171 4.1 36.5 + - - -
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 4.5 12.8 - - + -
155A PRO* 4.4 10.5 - - + -
156A SER 4.5 6.5 - - - +
157A VAL* 4.8 4.9 - - + -
300A VAL* 3.0 19.6 + - + +
301A ALA 3.6 4.3 - - - +
303A ARG* 1.3 79.4 - - + +
305A LEU* 1.3 63.2 + - - +
307A LYS* 3.3 11.6 + - + +
308A TYR* 2.7 39.3 + - + -
314A VAL* 3.5 33.0 - - + -
316A SER 3.6 8.3 - - - +
317A SER 3.7 19.7 - - - +
319A VAL* 4.1 16.6 - - + -
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 4.3 5.8 - - + -
119A GLY* 3.8 4.9 - - - +
120A ILE 3.7 17.3 - - - +
121A ILE* 3.6 30.3 - - + -
141A PRO* 3.3 35.7 - - + +
143A VAL* 3.5 23.7 - - + +
301A ALA 2.9 19.6 + - - +
302A MET* 3.9 5.2 - - - +
304A LEU* 1.3 76.3 - - - +
306A THR* 1.3 57.5 + - - +
308A TYR* 3.3 6.4 + - - +
309A MET* 2.8 50.6 + - + +
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Residues in contact with THR 306 (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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89A TYR* 3.3 19.9 - - + -
91A TYR* 2.7 33.8 + - - +
302A MET 2.7 27.3 + - - -
303A ARG* 3.6 5.2 - - - -
305A LEU* 1.3 70.5 - - - +
307A LYS* 1.3 69.1 + - + +
309A MET* 3.0 11.4 + - + +
310A ASN* 2.8 38.8 + - - +
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Residues in contact with LYS 307 (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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303A ARG* 2.8 39.5 + - - +
304A LEU* 3.4 11.2 - - + +
306A THR* 1.3 76.7 - - - +
308A TYR* 1.3 65.7 + - - +
310A ASN 3.0 5.5 + - - -
312A GLU* 2.9 57.5 + - + +
313A THR 4.1 18.5 + - - +
314A VAL* 4.3 17.9 - - + -
315A ASP* 5.4 5.8 + - - -
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Residues in contact with TYR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PRO* 3.4 29.2 - - + +
143A VAL* 4.2 7.2 - - + -
155A PRO* 3.5 20.7 - - + +
304A LEU* 2.7 40.3 + - + -
305A LEU* 3.3 9.9 - - - +
306A THR 3.1 0.4 - - - -
307A LYS* 1.3 78.9 - - - +
309A MET* 1.3 54.5 + - - +
311A LYS* 2.6 30.7 + - - +
312A GLU 4.6 9.6 - - - +
314A VAL* 3.2 34.5 - - + +
317A SER* 2.9 27.0 + - - -
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Residues in contact with MET 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 4.0 16.4 - - + -
63A VAL* 4.3 10.5 - - + -
91A TYR* 4.6 6.7 - - + +
118A ASP* 3.1 47.8 - - + +
119A GLY* 4.0 4.5 - - - -
141A PRO* 4.0 8.7 - - + +
302A MET* 5.8 0.4 - - - -
305A LEU* 2.8 58.9 + - + +
306A THR* 3.0 17.0 + - + +
308A TYR* 1.3 72.7 - - - +
310A ASN* 1.3 65.1 + - - +
311A LYS* 3.3 15.6 + - - +
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Residues in contact with ASN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 2.8 32.5 + - - +
307A LYS 3.8 0.7 - - - +
308A TYR 2.9 0.2 + - - -
309A MET* 1.3 80.6 + - - +
311A LYS* 1.3 71.7 + - - +
312A GLU* 3.2 29.5 + - - +
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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
------------------------------------------------------------
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