Contacts of the helix formed by residues 306 - 324 (chain B) in PDB entry 3N9Z
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 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B GLU* 2.7 44.0 + - - +
303B MET 3.3 6.7 - - - +
305B ARG* 1.3 98.7 + - - +
307B LEU* 1.3 58.9 + - - +
308B LYS* 3.3 3.4 - - - -
309B VAL* 3.1 22.1 + - + +
310B GLN 3.0 21.8 + - - -
395B ASN* 4.2 15.1 - - - +
396B PHE* 3.5 18.8 + - + +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET 3.9 2.2 - - - +
304B ALA 3.7 20.2 - - - +
305B ARG 3.8 1.9 + - - -
306B ASN* 1.3 74.4 - - - +
308B LYS* 1.3 61.9 + - + +
310B GLN* 3.3 24.6 + - - +
311B ASP* 2.9 36.9 + - - +
446B VAL 4.0 8.7 - - - +
447B GLU* 4.7 19.3 - - + +
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASN 3.3 0.8 - - - -
307B LEU* 1.3 76.9 - - + +
309B VAL* 1.3 69.2 + - + +
311B ASP* 3.3 13.4 + - - +
312B MET* 3.0 29.0 + - - +
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 5.5 1.3 - - + -
306B ASN* 3.1 21.1 + - + +
308B LYS* 1.3 75.6 - - + +
310B GLN* 1.3 64.3 + - - +
312B MET* 3.2 16.8 + - + +
313B LEU* 3.0 34.3 + - + +
337B LEU* 6.1 1.6 - - + -
396B PHE* 3.7 46.0 - - + +
397B ASP* 5.3 2.9 - - - +
398B PRO* 3.9 20.4 - - + -
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Residues in contact with GLN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 2.9 53.6 - - + +
306B ASN 3.0 6.1 + - - -
307B LEU* 3.5 17.9 - - - +
308B LYS 3.3 0.2 - - - -
309B VAL* 1.3 76.6 - - - +
311B ASP* 1.3 56.5 + - - +
313B LEU* 3.4 2.3 + - - +
314B ARG* 2.9 62.2 + - - +
441B LEU* 4.1 2.0 - - + +
445B ARG* 3.6 4.0 - - - +
446B VAL* 2.9 51.7 + - - +
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Residues in contact with ASP 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 2.9 24.4 + - - +
308B LYS* 3.5 13.6 - - - +
309B VAL 3.3 0.2 - - - -
310B GLN* 1.3 73.1 - - - +
312B MET* 1.3 60.4 + - + +
314B ARG* 3.4 19.1 + - - +
315B ALA* 3.0 31.4 + - - +
445B ARG* 5.5 5.5 + - - -
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LYS* 3.0 19.4 + - - +
309B VAL* 3.2 18.6 + - + +
311B ASP* 1.3 75.4 - - + +
313B LEU* 1.3 62.8 + - - +
315B ALA* 3.5 5.9 + - - +
316B GLU* 3.1 23.6 + - - +
337B LEU* 3.7 28.8 - - + +
399B THR* 4.3 20.9 - - + -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B HIS* 4.0 5.8 - - + +
303B MET* 3.7 26.9 - - + -
309B VAL* 3.0 34.4 + - + +
310B GLN 3.8 3.8 - - - +
312B MET* 1.3 75.3 - - - +
314B ARG* 1.3 61.5 + - - +
316B GLU* 3.3 5.9 + - - +
317B VAL* 3.0 27.7 + - - +
337B LEU* 3.5 48.2 - - + +
338B LEU* 3.8 13.0 - - + +
341B SER* 3.9 17.5 - - - +
396B PHE* 5.1 0.4 - - + -
398B PRO* 4.9 2.5 - - + -
441B LEU* 3.8 15.9 - - + -
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Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLN* 2.9 48.4 + - - +
311B ASP* 3.8 22.4 + - - +
313B LEU* 1.3 76.4 - - - +
315B ALA* 1.3 56.9 + - - +
317B VAL* 3.2 2.8 + - - +
318B LEU* 2.9 47.1 + - + +
441B LEU* 2.8 45.4 + - + +
444B PHE 2.6 26.6 + - - -
445B ARG* 3.5 19.9 - - - +
475B PHE* 3.6 34.1 - - + -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ASP 3.0 19.1 + - - +
312B MET* 3.8 5.8 - - - +
314B ARG* 1.3 76.4 - - - +
316B GLU* 1.3 61.5 + - - +
318B LEU* 4.0 9.7 - - - +
319B ALA* 3.1 24.3 + - - +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B MET 3.1 16.5 + - - +
313B LEU* 3.7 6.6 - - - +
314B ARG 3.2 0.2 - - - -
315B ALA* 1.3 77.3 - - - +
317B VAL* 1.3 56.6 + - - +
319B ALA* 3.5 5.4 + - + +
320B ALA* 2.9 28.3 + - - +
334B LEU 4.0 9.5 - - - +
335B VAL* 3.4 18.8 - - - +
336B PRO* 3.2 14.9 - - - +
337B LEU* 2.9 34.3 + - + +
338B LEU* 3.1 26.7 + - - +
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU 3.0 20.8 + - - +
314B ARG* 3.2 6.0 + - - +
316B GLU* 1.3 75.0 - - + +
318B LEU* 1.3 60.2 + - + +
320B ALA 3.2 0.7 + - - -
321B ARG* 2.9 26.3 + - - +
331B MET* 3.4 18.8 - - + +
335B VAL* 4.2 13.7 - - + -
338B LEU* 3.8 30.1 - - + -
438B ILE* 3.8 15.5 - - + +
441B LEU* 3.9 15.0 - - + -
442B GLU* 3.7 26.5 - - + +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ARG* 2.9 29.0 + - + +
315B ALA* 4.0 7.2 - - - +
317B VAL* 1.3 76.1 - - + +
319B ALA* 1.3 61.7 + - - +
321B ARG* 3.5 5.7 + - + +
322B HIS* 3.2 23.2 + - - +
442B GLU* 4.2 26.5 - - + +
475B PHE* 3.8 36.6 - - + -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA 3.1 19.2 + - - +
316B GLU* 3.7 7.4 - - + +
317B VAL 3.3 0.2 - - - -
318B LEU* 1.3 75.0 - - - +
320B ALA* 1.3 58.1 + - - +
322B HIS* 3.4 4.8 + - - +
323B GLN* 2.9 44.8 + - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLU 2.9 18.1 + - - +
317B VAL 3.2 4.7 + - - +
319B ALA* 1.3 74.3 - - - +
321B ARG* 1.3 65.3 + - - +
323B GLN* 3.8 1.2 - - - +
324B ALA* 2.9 27.9 + - - +
331B MET* 3.6 10.3 - - + +
334B LEU* 3.7 39.1 - - + +
335B VAL* 3.7 14.4 - - + -
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Residues in contact with ARG 321 (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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133B ASP* 5.2 3.4 + - - -
137B ARG* 6.1 0.6 - - - +
317B VAL 2.9 13.3 + - - +
318B LEU* 3.8 7.2 - - + +
319B ALA 3.3 0.2 - - - -
320B ALA* 1.3 76.8 - - - +
322B HIS* 1.3 61.5 + - - +
324B ALA* 3.5 0.5 + - - +
325B GLN 3.1 3.6 + - - -
326B GLY* 3.0 64.9 + - - -
328B MET* 3.8 18.4 - - - +
331B MET* 3.5 23.6 - - + +
438B ILE* 3.8 12.5 - - - +
439B ASN* 4.2 9.9 + - - -
442B GLU* 2.7 46.0 + - - +
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Residues in contact with HIS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU 3.2 14.6 + - - +
319B ALA* 3.7 4.3 - - - +
321B ARG* 1.3 79.2 - - - +
323B GLN* 1.3 93.8 + - - +
325B GLN* 3.1 20.1 + - - +
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Residues in contact with GLN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ALA* 2.9 38.6 + - - +
320B ALA* 3.9 2.9 - - - +
322B HIS* 1.3 102.1 + - - +
324B ALA* 1.3 60.4 + - - +
325B GLN* 3.2 9.3 + - - +
330B THR* 5.3 0.7 - - - +
334B LEU* 3.9 17.5 - - + -
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ALA 2.9 17.4 + - - +
321B ARG 4.0 3.1 - - - +
323B GLN* 1.3 75.5 - - - +
325B GLN* 1.3 69.7 + - - +
326B GLY 4.4 0.2 - - - +
327B ASP* 3.3 38.8 + - - +
330B THR* 3.7 19.2 + - + +
331B MET* 3.6 18.8 - - + +
334B LEU* 4.2 2.0 - - + +
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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
------------------------------------------------------------
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