Contacts of the helix formed by residues 305 - 318 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA* 3.9 18.6 - - + -
29B ILE* 5.0 0.4 - - + -
43B GLU* 2.8 19.1 + - - +
304B SER* 1.3 95.1 + - - +
306B GLY* 1.3 64.2 + - - +
307B ILE* 3.0 23.3 + - - +
308B LEU* 3.4 4.3 + - - +
309B LEU* 3.3 18.1 + - - +
334B LEU* 3.5 27.6 - - + +
335B PHE* 4.3 10.5 - - - +
338B LEU* 3.9 16.2 - - + -
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Residues in contact with GLY 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR* 1.3 72.7 - - - +
307B ILE* 1.3 58.2 + - - +
309B LEU* 3.7 7.0 - - - -
310B HIS* 2.8 36.9 + - - +
334B LEU 4.7 0.4 + - - -
335B PHE 4.2 1.2 + - - -
339B VAL* 3.6 15.4 - - - +
342B GLN* 3.4 38.0 + - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 3.5 30.5 - - + -
41B VAL* 3.6 31.9 - - + +
42B GLY* 3.7 29.6 - - - -
43B GLU* 3.6 10.3 - - + +
108B ILE* 4.5 6.7 - - + -
305B THR* 3.0 15.0 + - - +
306B GLY* 1.3 76.2 - - - +
308B LEU* 1.3 66.3 + - - +
310B HIS* 3.2 1.7 + - - +
311B ALA* 3.0 22.9 + - - +
338B LEU* 4.0 10.1 - - + -
339B VAL* 3.6 12.3 - - + +
360B ILE* 3.9 14.7 - - + +
362B LEU* 4.2 3.1 - - + -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 3.1 19.0 + - - +
45B ASP* 4.8 1.6 - - + -
274B ASP* 3.8 7.0 - - - +
275B ILE* 4.4 2.7 - - + -
276B THR* 3.7 38.1 - - + +
301B HIS 4.7 1.1 - - - +
302B GLY* 3.6 42.0 - - - +
303B PHE* 3.8 8.7 - - - +
304B SER* 4.2 14.6 - - - +
305B THR 3.4 6.5 + - - +
307B ILE* 1.3 74.7 - - - +
309B LEU* 1.3 61.7 + - + +
311B ALA* 3.4 4.8 + - - +
312B SER* 2.8 49.7 + - - +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR 3.3 10.9 + - - +
306B GLY* 3.6 6.7 - - - +
307B ILE 3.2 0.4 - - - -
308B LEU* 1.3 83.6 - - + +
310B HIS* 1.3 61.3 + - + +
312B SER* 3.3 3.1 + - - -
313B VAL* 3.0 41.6 + - + +
325B MET* 3.7 31.0 - - + -
326B GLU 5.4 1.6 - - - +
327B PHE* 3.8 24.7 - - + -
335B PHE* 5.5 4.9 - - + -
342B GLN* 4.0 22.7 - - + +
343B LEU* 3.5 33.7 - - + +
350B VAL* 4.9 1.6 - - + -
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Residues in contact with HIS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLY* 2.8 30.1 + - - +
307B ILE 3.9 2.5 - - - +
309B LEU* 1.3 78.8 - - + +
311B ALA* 1.3 62.7 + - - +
313B VAL* 3.6 0.9 + - - +
314B HIS* 3.1 33.3 + - - -
339B VAL* 4.1 12.7 - - + +
341B ASN 4.3 7.4 - - - -
342B GLN* 3.7 4.8 - - - -
343B LEU* 3.1 55.3 + - + +
353B SER* 5.6 3.3 - - - -
358B LEU* 2.9 28.7 + - + +
359B GLY* 3.2 20.5 + - - -
360B ILE* 3.6 14.3 - - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 4.1 26.5 - - + -
275B ILE* 3.8 20.0 - - + +
281B ILE* 4.2 13.8 - - + +
307B ILE 3.0 16.3 + - - +
308B LEU* 3.8 4.3 - - - +
310B HIS* 1.3 77.6 - - - +
312B SER* 1.3 57.7 + - - +
314B HIS* 3.5 1.6 + - - +
315B PHE* 3.0 29.3 + - - +
358B LEU* 3.9 12.4 - - + +
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 3.5 23.2 - - - +
300B PRO* 5.0 15.8 - - - +
301B HIS 5.2 2.1 + - - -
308B LEU* 2.8 33.8 + - - +
309B LEU* 3.3 3.6 + - - -
311B ALA* 1.3 76.7 - - - +
313B VAL* 1.3 57.7 + - - +
315B PHE* 3.4 1.7 + - - +
316B LEU* 2.9 34.6 + - - +
325B MET* 4.2 20.2 - - - -
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 3.6 19.4 - - + +
309B LEU* 3.0 27.1 + - + +
310B HIS 4.0 3.1 - - - +
312B SER* 1.3 73.9 - - - +
314B HIS* 1.3 68.0 + - + +
317B ALA* 2.9 25.3 + - - +
325B MET* 3.6 28.3 - - + -
343B LEU* 4.0 20.6 - - + -
350B VAL* 4.1 13.7 - - + +
351B ALA 4.1 10.8 - - - +
352B VAL* 4.1 16.8 - - + -
353B SER 4.7 1.3 - - - +
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Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PRO* 3.6 15.3 - - + -
122B VAL* 3.6 14.5 + - + -
123B HIS* 3.2 43.7 + + - +
126B LEU* 3.8 6.2 - - - +
310B HIS* 3.1 26.6 + + - +
311B ALA 3.9 3.1 - - - +
313B VAL* 1.3 80.6 - - + +
315B PHE* 1.3 63.9 + - - +
317B ALA* 4.6 1.1 - - - -
318B ALA 3.5 4.0 + - - -
343B LEU* 6.1 1.6 - - + -
352B VAL* 6.2 0.2 - - + -
353B SER* 3.4 33.8 + - - -
355B ALA 4.1 3.2 + - - -
357B GLY 3.1 22.1 + - - -
358B LEU* 3.6 36.5 + - + -
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Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.8 19.4 - - + +
275B ILE* 3.8 13.7 - - + -
281B ILE* 4.6 6.7 - - + +
284B MET* 3.4 51.6 - - + -
285B LYS* 3.7 27.4 - - + -
288B TYR* 3.8 16.2 - + + -
298B LEU* 4.6 8.1 - - + -
300B PRO* 5.0 4.3 - - + -
311B ALA 3.0 18.1 + - - +
312B SER 3.6 4.3 - - - +
314B HIS* 1.3 76.1 - - - +
316B LEU* 1.3 75.0 + - + +
318B ALA* 3.1 14.7 + - - +
319B CYS* 3.3 38.9 + - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ARG* 2.9 21.4 + - - -
134B ILE* 3.8 15.3 - - + -
288B TYR* 6.2 0.7 - - + -
298B LEU* 4.8 7.6 - - + +
300B PRO* 3.8 34.8 - - + -
312B SER 2.9 23.0 + - - +
315B PHE* 1.3 85.1 - - + +
317B ALA* 1.3 60.4 + - - +
319B CYS* 3.0 12.5 + - + +
322B GLY* 3.5 27.7 - - - +
324B LEU 3.8 12.6 - - - +
325B MET* 3.7 35.7 - - + -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 4.0 9.2 - - + -
129B LYS* 3.3 7.6 - - + -
130B TYR* 2.8 35.3 + - - +
131B ARG* 3.8 12.7 + - - +
134B ILE* 4.0 2.7 - - - +
313B VAL 2.9 19.0 + - - +
314B HIS 3.8 5.6 - - - +
316B LEU* 1.3 76.1 - - - +
318B ALA* 1.3 55.8 + - - +
319B CYS 3.5 0.7 + - - -
352B VAL* 3.9 33.0 - - + -
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 3.5 25.1 - - + +
126B LEU* 3.5 33.3 - - + +
127B GLY* 5.4 0.7 - - - -
128B GLY 3.5 11.4 + - - +
130B TYR* 3.4 14.8 - - - -
314B HIS 3.5 6.2 + - - +
315B PHE 3.1 10.9 + - - +
317B ALA* 1.3 77.6 - - - +
319B CYS* 1.3 59.4 + - - +
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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