Contacts of the helix formed by residues 306 - 317 (chain B) in PDB entry 3NDM
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 SER 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLU* 2.6 36.7 + - - -
303B ASN* 5.6 0.2 - - - -
305B ILE* 1.3 75.7 - - - +
307B LYS* 1.3 64.7 + - - +
308B GLU* 3.6 7.4 - - - -
309B ALA* 3.6 10.8 - - - +
310B LYS* 3.1 28.4 + - - +
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Residues in contact with LYS 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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305B ILE 4.2 0.6 + - - -
306B SER* 1.3 74.5 - - - +
308B GLU* 1.3 73.7 + - - +
310B LYS* 3.9 7.5 - - + +
311B ASN* 3.0 49.6 + - - +
336B LEU* 6.1 0.2 - - - -
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Residues in contact with GLU 308 (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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306B SER* 3.0 6.8 - - - -
307B LYS* 1.3 100.8 + - + +
309B ALA* 1.3 64.3 + - - +
311B ASN* 4.2 7.1 + - - +
312B LEU* 3.2 16.3 + - - +
335B HIS* 3.4 12.1 + - - -
336B LEU* 2.7 58.9 - - + +
337B PHE* 3.2 32.8 - - + +
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Residues in contact with ALA 309 (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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172B GLU* 3.3 22.0 - - - +
268B LEU* 4.1 3.5 - - + +
272B LEU* 3.9 23.8 - - + -
305B ILE* 4.9 3.1 - - + -
306B SER* 3.4 12.9 + - - +
308B GLU* 1.3 76.4 - - - +
310B LYS* 1.3 65.9 + - - +
312B LEU* 3.2 4.7 + - - +
313B ILE* 3.0 28.4 + - + +
337B PHE* 3.5 15.7 - - + -
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Residues in contact with LYS 310 (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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299B PHE* 4.3 26.9 - - + -
303B ASN* 2.6 33.9 + - - +
305B ILE* 3.8 21.8 - - + -
306B SER 3.1 17.0 + - - +
307B LYS* 3.9 7.4 - - + +
309B ALA* 1.3 79.6 - - - +
311B ASN* 1.3 68.2 + - - +
312B LEU 2.8 1.7 + - - -
313B ILE* 3.0 4.0 + - - -
314B CYS* 2.9 39.4 + - - -
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Residues in contact with ASN 311 (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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307B LYS* 3.0 33.9 + - - +
308B GLU* 4.2 9.5 + - - +
309B ALA 3.4 0.2 - - - -
310B LYS* 1.3 78.1 - - - +
312B LEU* 1.3 57.3 + - - +
314B CYS* 4.6 1.7 - - - -
315B ALA* 3.1 24.1 + - - +
335B HIS* 3.8 20.3 - - + -
336B LEU* 6.1 1.4 - - - +
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Residues in contact with LEU 312 (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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179B THR* 4.7 3.4 - - + -
268B LEU* 3.4 26.7 - - + -
308B GLU 3.2 14.4 + - - +
309B ALA 3.3 8.3 - - - +
310B LYS 2.8 1.0 + - - -
311B ASN* 1.3 76.4 - - - +
313B ILE* 1.3 54.5 + - - +
315B ALA* 2.7 32.0 + - - +
316B PHE* 3.1 37.7 + - + -
324B LEU* 3.5 21.1 - - + -
332B ILE* 5.0 2.2 - - + -
335B HIS* 3.5 19.7 - - + +
337B PHE* 3.7 21.5 - - + -
338B PHE* 4.3 10.3 - - + -
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Residues in contact with ILE 313 (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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265B GLY* 4.0 10.5 - - - +
268B LEU* 3.3 29.4 - - + +
269B TYR* 3.7 38.6 - - + +
272B LEU* 5.3 5.8 - - + -
273B VAL* 6.1 0.7 - - + -
297B LEU* 5.1 1.3 - - + -
299B PHE* 4.3 17.5 - - + -
309B ALA* 3.0 11.9 + - + +
310B LYS* 3.7 3.1 - - - +
312B LEU* 1.3 73.8 - - - +
314B CYS* 1.3 74.3 + - - +
315B ALA 2.8 5.8 + - - -
316B PHE* 2.9 9.3 + - - +
317B LEU* 2.8 48.6 + - + +
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Residues in contact with CYS 314 (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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297B LEU* 4.3 21.1 - - + -
299B PHE* 3.7 23.3 - - - -
310B LYS* 2.9 26.3 + - - +
311B ASN* 4.6 2.0 - - - +
313B ILE* 1.3 85.9 - - - +
315B ALA* 1.3 51.0 + - - +
317B LEU* 4.5 1.9 - - - +
318B THR* 2.6 27.6 - - - +
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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
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311B ASN 3.1 16.8 + - - +
312B LEU* 2.7 14.6 + - - +
314B CYS* 1.3 80.2 - - - +
316B PHE* 1.3 58.4 + - - +
318B THR* 3.4 17.6 + - - +
322B VAL 4.5 0.2 - - - +
323B ARG* 3.6 0.5 - - - +
324B LEU* 2.9 43.7 + - + +
335B HIS* 5.7 0.7 - - + -
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Residues in contact with PHE 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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179B THR* 5.6 0.2 - - + -
183B VAL* 5.4 2.7 - - + -
261B TRP* 3.8 32.1 - + + +
262B TRP* 3.6 5.9 - - - -
264B VAL* 3.2 31.9 - - + -
265B GLY* 3.8 20.4 - - - -
268B LEU* 5.8 0.7 - - + -
312B LEU* 3.1 38.5 + - + -
313B ILE* 2.9 6.9 + - - +
315B ALA* 1.3 77.3 - - - +
317B LEU* 1.3 60.0 + - + +
318B THR 3.0 7.4 + - - -
323B ARG* 2.9 29.3 + - + -
324B LEU* 3.6 33.4 - - + -
332B ILE* 3.7 31.2 - - + -
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Residues in contact with LEU 317 (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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262B TRP* 3.5 31.6 - - + +
265B GLY* 3.2 40.4 - - - +
266B VAL* 3.6 3.1 - - + +
269B TYR* 4.8 1.3 - - + -
277B PRO* 4.0 24.2 - - + -
278B PHE* 4.2 13.9 - - + -
293B HIS* 3.4 17.3 - - - +
294B LYS* 5.8 0.2 - - - -
297B LEU* 4.0 34.8 - - + +
313B ILE* 2.8 30.5 + - + +
314B CYS* 4.6 1.2 - - - +
316B PHE* 1.3 75.9 - - - +
318B THR* 1.3 60.1 + - - +
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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