Contacts of the helix formed by residues 305 - 318 (chain A) in PDB entry 3SJN
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 THR 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.0 15.7 - - + -
29A ILE* 5.2 0.2 - - + -
43A GLU* 2.6 23.7 + - - +
304A SER* 1.3 96.1 + - - +
306A GLY* 1.3 62.6 + - - +
307A ILE* 3.0 20.3 + - - +
308A LEU* 3.5 4.7 + - - +
309A LEU* 3.4 17.0 + - - +
334A LEU* 3.6 23.8 - - + +
335A PHE* 4.3 11.6 - - - +
338A LEU* 3.7 23.6 - - + -
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Residues in contact with GLY 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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305A THR* 1.3 73.6 - - - +
307A ILE* 1.3 55.2 + - - +
309A LEU* 3.7 5.8 - - - -
310A HIS* 2.8 39.7 + - - +
334A LEU 4.6 0.4 + - - -
335A PHE 4.2 0.8 + - - -
339A VAL* 3.7 16.2 - - - +
342A GLN* 3.3 38.0 + - - +
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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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29A ILE* 3.6 29.4 - - + -
41A VAL* 3.7 30.7 - - + +
42A GLY* 3.7 31.6 - - - +
43A GLU* 3.5 8.7 - - + +
108A ILE* 4.5 6.5 - - + -
305A THR* 3.0 15.8 + - - +
306A GLY* 1.3 73.9 - - - +
308A LEU* 1.3 64.2 + - - +
310A HIS* 3.9 1.4 - - - +
311A ALA* 3.0 24.5 + - - +
338A LEU* 4.0 10.3 - - + -
339A VAL* 3.6 13.2 - - + +
360A ILE* 3.9 14.9 - - + +
362A LEU* 4.1 5.4 - - + -
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Residues in contact with LEU 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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43A GLU* 3.1 17.8 + - - +
45A ASP* 4.9 1.6 - - + -
274A ASP* 3.7 19.5 - - - +
275A ILE* 4.2 3.5 - - + +
276A THR* 3.7 27.1 - - + +
301A HIS 4.6 1.1 - - - +
302A GLY* 3.6 41.3 - - - +
303A PHE* 3.8 9.0 - - - +
304A SER* 4.2 13.9 - - - +
305A THR 3.5 6.3 + - - +
306A GLY 3.4 0.2 - - - -
307A ILE* 1.3 74.4 - - - +
309A LEU* 1.3 60.6 + - + +
311A ALA* 3.8 4.0 - - - +
312A SER* 2.7 50.8 + - - +
326A GLU 6.1 0.2 - - - +
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Residues in contact with LEU 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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305A THR 3.4 11.1 + - - +
306A GLY* 3.3 7.8 + - - +
307A ILE 3.2 0.4 - - - -
308A LEU* 1.3 85.0 - - + +
310A HIS* 1.3 61.2 + - + +
312A SER* 3.2 3.3 + - - -
313A VAL* 2.9 43.0 + - + +
325A MET* 3.5 33.0 - - + -
326A GLU 5.4 1.3 - - - +
327A PHE* 3.9 22.2 - - + -
335A PHE* 5.6 4.7 - - + -
342A GLN* 4.1 20.9 - - + +
343A LEU* 3.5 34.1 - - + +
350A VAL* 4.9 1.8 - - + -
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Residues in contact with HIS 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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306A GLY* 2.8 32.4 + - - +
309A LEU* 1.3 78.9 - - + +
311A ALA* 1.3 62.4 + - - +
313A VAL* 4.0 4.4 - - - +
314A HIS* 3.1 33.7 + + + -
339A VAL* 4.1 7.5 - - + +
341A ASN 4.2 8.7 - - - -
342A GLN* 3.6 6.2 - - - -
343A LEU* 3.1 52.2 + - + +
353A SER* 5.4 4.2 - - - -
358A LEU* 2.8 27.9 + - + +
359A GLY* 3.2 20.7 + - - -
360A ILE* 3.7 17.4 - - + +
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Residues in contact with ALA 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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108A ILE* 4.1 25.4 - - + -
275A ILE* 3.9 19.0 - - + +
281A ILE* 4.3 14.8 - - + +
307A ILE 3.0 18.1 + - - +
308A LEU* 3.9 3.4 - - - +
310A HIS* 1.3 77.7 - - - +
312A SER* 1.3 57.2 + - - +
314A HIS* 3.8 2.1 - - - +
315A PHE* 3.0 28.9 + - - +
358A LEU* 3.9 13.1 - - + +
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Residues in contact with SER 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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275A ILE* 3.6 20.6 - - - +
300A PRO* 4.9 15.5 - - - +
301A HIS 5.2 1.6 + - - -
308A LEU* 2.7 41.5 + - - +
309A LEU* 3.8 2.7 - - - -
311A ALA* 1.3 72.9 - - - +
313A VAL* 1.3 58.6 + - - +
315A PHE* 3.4 2.0 + - - +
316A LEU* 2.9 34.3 + - - +
325A MET* 4.2 20.0 - - - -
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Residues in contact with VAL 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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134A ILE* 3.5 19.2 - - + +
309A LEU* 2.9 26.9 + - + +
310A HIS 4.0 3.6 - - - +
312A SER* 1.3 73.6 - - - +
314A HIS* 1.3 69.4 + - + +
316A LEU 3.4 0.2 + - - -
317A ALA* 2.9 24.6 + - - +
325A MET* 3.6 21.5 - - - -
343A LEU* 4.0 24.7 - - + -
350A VAL* 3.8 18.2 - - + -
351A ALA 4.1 10.8 - - - +
352A VAL* 4.1 13.0 - - + -
353A SER 4.7 2.0 - - - +
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Residues in contact with HIS 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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121A PRO* 3.5 15.9 - - + -
122A VAL* 3.7 18.4 + - + -
123A HIS* 3.2 46.0 + + - +
126A LEU* 3.9 2.6 - - - +
310A HIS* 3.1 28.0 + - - +
311A ALA 3.8 3.6 - - - +
313A VAL* 1.3 81.4 - - + +
315A PHE* 1.3 63.9 + - - +
317A ALA* 4.6 1.1 - - - -
318A ALA* 3.4 7.6 + - - +
343A LEU* 6.1 0.9 - - + -
352A VAL* 5.8 0.2 - - + -
353A SER* 3.5 31.8 + - - -
355A ALA 4.2 2.6 + - - -
357A GLY 3.1 23.3 + - - -
358A LEU* 3.6 32.6 + - + -
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Residues in contact with PHE 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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126A LEU* 3.8 21.2 - - + +
275A ILE* 3.8 11.2 - - + -
281A ILE* 4.4 11.2 - - + +
284A MET* 3.4 49.1 - - + -
285A LYS* 3.7 31.0 - - + -
288A TYR* 3.8 16.4 - + + -
298A LEU* 4.6 7.2 - - + -
300A PRO* 5.3 3.1 - - + -
311A ALA 3.0 18.4 + - - +
312A SER* 3.7 3.6 - - - +
313A VAL 3.2 0.2 - - - -
314A HIS* 1.3 76.7 - - - +
316A LEU* 1.3 73.8 + - + +
318A ALA* 3.1 14.4 + - + +
319A CYS* 3.3 37.9 + - - -
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Residues in contact with LEU 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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131A ARG* 2.8 27.8 + - - -
134A ILE* 3.9 18.4 - - + -
288A TYR* 6.4 0.4 - - + -
298A LEU* 4.9 7.4 - - + +
300A PRO* 3.7 29.2 - - + -
312A SER 2.9 23.0 + - - +
315A PHE* 1.3 81.7 - - + +
317A ALA* 1.3 57.3 + - - +
319A CYS* 3.0 11.6 + - - +
322A GLY* 3.5 26.4 - - - +
324A LEU 3.5 24.0 - - - +
325A MET* 3.7 28.9 - - + -
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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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123A HIS* 4.0 9.6 - - + -
129A LYS* 4.1 8.3 - - + -
130A TYR* 2.8 32.6 + - - -
131A ARG* 3.7 11.6 + - - +
134A ILE* 3.9 5.5 - - - +
313A VAL 2.9 18.5 + - - +
314A HIS 3.7 5.8 - - - +
316A LEU* 1.3 76.4 - - - +
318A ALA* 1.3 56.6 + - - +
319A CYS 3.5 1.2 + - - -
352A VAL* 3.9 33.0 - - + -
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Residues in contact with ALA 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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123A HIS* 3.7 13.9 - - + +
126A LEU* 3.5 39.7 - - + +
127A GLY* 5.5 0.9 - - - -
128A GLY 3.4 11.9 + - - +
130A TYR* 3.5 13.1 - - - -
314A HIS 3.4 8.5 + - - +
315A PHE* 3.1 12.0 + - + +
316A LEU 3.1 0.8 - - - -
317A ALA* 1.3 78.2 - - - +
319A CYS* 1.3 59.0 + - - +
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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