Contacts of the helix formed by residues 302 - 316 (chain A) in PDB entry 1SXQ
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 ASN 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GLU* 3.2 15.9 - - - +
202A PHE* 3.4 18.9 - - - -
300A VAL* 3.6 1.3 - - - +
301A ASN* 1.3 82.7 - - - +
303A ARG* 1.3 64.4 + - - +
304A ALA* 3.3 12.8 + - - +
305A GLU* 2.9 31.6 + - - +
306A LEU 3.1 16.3 + - - -
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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
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200A VAL* 2.8 39.6 + - - +
201A GLU* 2.9 43.7 + - - +
202A PHE* 4.5 5.2 - - - +
204A PHE* 3.1 15.6 + - - +
205A ASP* 3.6 34.8 + - - +
206A THR* 4.4 8.7 - - + -
227A PRO 5.2 1.8 + - - -
302A ASN* 1.3 76.7 - - - +
304A ALA* 1.3 63.5 + - - +
306A LEU* 3.1 4.9 + - - +
307A ILE* 2.9 41.8 + - + +
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Residues in contact with ALA 304 (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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302A ASN* 3.3 14.3 + - - +
303A ARG* 1.3 78.3 - - - +
305A GLU* 1.3 65.6 + - + +
307A ILE* 3.3 11.2 + - - +
308A ASP* 3.0 24.3 + - - +
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Residues in contact with GLU 305 (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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299A TYR 4.6 2.3 - - - +
300A VAL* 3.8 11.5 - - + +
301A ASN* 2.8 50.3 + - - +
302A ASN* 2.9 23.7 + - - +
304A ALA* 1.3 77.2 - - + +
306A LEU* 1.3 57.9 + - - +
308A ASP* 3.8 6.5 - - - +
309A ARG* 2.9 43.7 + - - +
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Residues in contact with LEU 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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184A VAL* 4.9 17.0 - - + -
202A PHE* 3.1 49.4 - - + +
206A THR* 5.2 5.2 - - + -
208A LEU* 5.2 1.8 - - + -
210A ILE* 5.4 0.7 - - + -
254A LEU* 4.7 7.9 - - + -
281A LEU* 3.4 39.7 - - + -
300A VAL* 3.9 15.8 - - + +
302A ASN 3.1 13.6 + - - +
303A ARG* 3.5 8.5 - - - +
305A GLU* 1.3 77.2 - - - +
307A ILE* 1.3 64.3 + - + +
309A ARG* 3.2 0.9 + - - +
310A VAL* 2.9 36.9 + - + +
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Residues in contact with ILE 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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205A ASP 4.7 1.3 - - - +
206A THR* 3.4 47.3 - - + +
208A LEU* 4.1 17.0 - - + +
303A ARG* 2.9 33.1 + - + +
304A ALA* 3.7 9.9 - - - +
306A LEU* 1.3 76.5 - - + +
308A ASP* 1.3 59.7 + - - +
310A VAL* 3.8 1.9 - - - +
311A ASN* 2.9 48.9 + - - +
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Residues in contact with ASP 308 (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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304A ALA 3.0 16.8 + - - +
305A GLU* 3.8 6.6 - - - +
307A ILE* 1.3 78.5 - - - +
309A ARG* 1.3 66.7 + - - +
311A ASN* 3.3 11.7 + - - +
312A GLU* 3.0 37.0 + - - +
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Residues in contact with ARG 309 (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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281A LEU* 3.8 26.0 - - + -
296A ALA 3.9 3.0 + - - -
297A ARG* 2.9 35.6 + - - +
299A TYR 2.9 28.1 + - - -
300A VAL* 3.8 12.0 - - + +
305A GLU* 2.9 35.8 + - - +
306A LEU 3.6 3.1 - - - +
308A ASP* 1.3 83.5 + - - +
310A VAL* 1.3 64.2 + - - +
312A GLU* 3.1 20.5 + - - +
313A LEU* 3.0 32.7 + - + +
319A LEU* 5.8 2.2 - - - -
323A MET* 5.4 4.3 - - + -
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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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183A ASP* 4.1 19.3 - - + +
184A VAL* 3.7 23.1 - - + -
208A LEU* 3.9 19.5 - - + -
251A ILE* 4.9 4.5 - - + -
252A ALA* 4.6 4.0 - - + -
281A LEU* 3.9 9.9 - - + -
306A LEU* 2.9 33.6 + - + +
307A ILE 3.8 3.4 - - - +
309A ARG* 1.3 73.4 - - - +
311A ASN* 1.3 61.2 + - - +
313A LEU* 3.1 7.9 + - - +
314A LYS* 2.9 46.0 + - + +
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Residues in contact with ASN 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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208A LEU* 4.0 15.8 - - - +
307A ILE* 2.9 38.6 + - - +
308A ASP* 3.5 11.0 - - - +
309A ARG 3.2 0.2 - - - -
310A VAL* 1.3 76.0 - - - +
312A GLU* 1.3 57.7 + - - +
314A LYS* 3.3 13.8 + - - +
315A HIS* 3.0 30.0 + - - +
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Residues in contact with GLU 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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297A ARG* 5.9 1.9 - - - -
308A ASP* 3.0 24.5 + - - +
309A ARG* 3.1 20.9 + - - +
311A ASN* 1.3 77.7 - - - +
313A LEU* 1.3 56.8 + - - +
315A HIS* 3.3 7.6 + - + +
316A SER* 2.9 31.6 + - - -
319A LEU* 3.3 27.9 - - + +
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Residues in contact with LEU 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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251A ILE* 3.7 24.0 - - + +
252A ALA* 4.3 11.4 - - + -
279A VAL* 4.1 28.5 - - + -
281A LEU* 4.4 12.6 - - + -
309A ARG* 3.0 21.7 + - + +
310A VAL* 3.1 8.5 + - - +
312A GLU* 1.3 74.8 - - - +
314A LYS* 1.3 63.2 + - - +
316A SER 3.3 18.8 + - - +
317A ASP* 4.2 1.4 + - - -
319A LEU* 4.0 8.5 - - + -
320A ARG* 3.8 40.9 - - + +
323A MET* 4.0 22.7 - - - -
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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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183A ASP* 2.7 40.0 + - - +
208A LEU* 4.8 4.0 - - + -
251A ILE* 4.5 18.5 - - + +
310A VAL* 2.9 30.9 + - + +
311A ASN* 3.7 15.7 - - - +
313A LEU* 1.3 77.0 - - - +
315A HIS* 1.3 61.7 + - - +
316A SER 5.1 0.5 - - - -
317A ASP* 5.1 1.0 + - - -
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Residues in contact with HIS 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 ASN 3.0 18.2 + - - +
312A GLU* 3.7 8.2 + - - +
314A LYS* 1.3 79.5 - - - +
316A SER* 1.3 63.3 + - - +
317A ASP 4.0 2.0 + - - -
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Residues in contact with SER 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 2.9 15.2 + - - -
313A LEU 3.3 10.0 - - - +
315A HIS* 1.3 84.7 - - - +
317A ASP* 1.3 63.5 + - - +
318A VAL* 3.6 9.9 + - - +
319A LEU* 3.0 29.2 + - - +
320A ARG 3.1 16.5 + - - -
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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
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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