Contacts of the helix formed by residues 310 - 322 (chain B) in PDB entry 1NYX
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 ASP 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309B LEU* 1.3 74.2 - - - +
311B LEU* 1.3 61.2 + - - +
312B ASN* 2.9 23.4 + - - +
313B ASP* 2.6 39.9 + - + +
314B GLN 2.8 12.1 + - - -
401B LEU* 2.9 37.2 - - + +
402B ASN* 5.6 5.2 - - + -
405B PRO* 6.3 0.2 - - - +
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Residues in contact with LEU 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 VAL 4.7 2.7 - - - +
309B LEU 3.9 4.9 - - - +
310B ASP* 1.3 74.2 + - - +
312B ASN* 1.3 63.7 + - - +
314B GLN* 3.5 26.2 - - - +
315B VAL* 2.9 34.0 + - + +
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Residues in contact with ASN 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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310B ASP* 2.9 21.4 + - - +
311B LEU* 1.3 78.1 - - - +
313B ASP* 1.3 63.8 + - - +
315B VAL* 3.7 6.0 + - - +
316B THR* 3.1 25.5 + - - -
399B GLY 6.1 0.4 - - - -
401B LEU* 4.2 16.3 - - + +
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Residues in contact with ASP 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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309B LEU* 4.7 6.5 - - + +
310B ASP* 2.6 31.5 + - + +
312B ASN* 1.3 71.4 - - - +
314B GLN* 1.3 66.6 + - - +
316B THR* 2.7 14.3 + - - -
317B LEU* 2.9 17.9 + - - +
399B GLY 4.4 0.7 - - - +
400B LEU* 3.3 22.4 - - + +
401B LEU* 2.8 29.9 + - - +
402B ASN* 3.2 34.6 + - - +
405B PRO* 5.5 0.7 - - - +
406B ILE* 4.1 8.0 - - + +
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Residues in contact with GLN 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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301B LYS* 5.6 3.6 - - - +
306B PHE* 3.2 56.9 - - + +
307B VAL* 2.7 34.4 + - - +
309B LEU* 2.9 22.3 + - + +
310B ASP 2.8 14.1 + - - +
311B LEU* 3.5 26.7 - - - +
313B ASP* 1.3 70.1 - - - +
315B VAL* 1.3 65.5 + - + +
317B LEU* 2.9 18.4 + - - +
318B LEU* 3.2 12.2 + - + +
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Residues in contact with VAL 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 LEU* 2.9 21.0 + - + +
312B ASN* 3.8 6.1 - - - +
314B GLN* 1.3 81.0 - - + +
316B THR* 1.3 60.0 + - - +
318B LEU* 3.5 8.6 + - - +
319B LYS* 3.0 31.4 + - + +
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Residues in contact with THR 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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312B ASN 3.1 14.9 + - - -
313B ASP* 2.7 13.4 + - - -
315B VAL* 1.3 73.3 - - - +
317B LEU* 1.3 63.4 + - - +
319B LYS* 4.6 2.7 - - - -
320B TYR* 3.0 37.8 + - + +
397B ARG* 4.1 3.5 - - + +
398B PRO 3.4 26.2 + - - +
399B GLY* 4.2 11.6 + - - -
400B LEU* 3.9 22.4 - - + -
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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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306B PHE* 3.5 27.1 - - + -
309B LEU* 3.9 21.1 - - + -
313B ASP 2.9 13.9 + - - +
314B GLN* 2.9 7.2 + - - +
316B THR* 1.3 76.0 - - - +
318B LEU* 1.3 63.1 + - + +
320B TYR* 4.4 0.2 - - - +
321B GLY* 2.9 24.8 + - - -
392B ILE* 3.5 30.0 - - - +
393B LEU* 4.2 9.4 - - + -
394B SER 4.5 0.7 - - - +
395B GLY 4.3 6.3 - - - +
397B ARG* 4.0 14.5 + - + -
400B LEU* 3.6 33.2 - - + -
406B ILE* 4.0 9.2 - - + -
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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
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293B VAL* 6.5 0.2 - - + -
296B ILE* 5.8 3.4 - - + -
297B THR* 3.7 39.0 - - + +
300B ALA* 4.1 6.7 - - + -
301B LYS* 6.4 0.4 - - + -
306B PHE* 3.7 28.7 - - + -
314B GLN 3.2 6.8 + - - +
315B VAL* 3.9 9.0 - - - +
317B LEU* 1.3 74.7 - - - +
319B LYS* 1.3 54.6 + - - +
320B TYR 2.6 16.3 + - - -
322B VAL* 2.9 39.4 + - + +
392B ILE* 3.5 30.3 - - + -
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Residues in contact with LYS 319 (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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315B VAL* 3.0 21.5 + - + +
316B THR* 4.2 5.4 - - - +
318B LEU* 1.3 77.1 - - - +
320B TYR* 1.3 97.2 + - + +
322B VAL* 5.1 4.5 - - - +
323B HIS* 5.1 9.5 + - - -
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Residues in contact with TYR 320 (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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316B THR* 3.0 36.3 + - + +
318B LEU 2.6 6.1 + - - -
319B LYS* 1.3 113.5 + - + +
321B GLY* 1.3 57.7 + - - +
322B VAL 3.5 2.2 + - - -
323B HIS* 4.5 8.8 + - - +
324B GLU* 4.6 5.2 - - - +
397B ARG* 3.4 33.6 + - + +
398B PRO* 3.4 43.7 + - + +
446B VAL* 5.7 1.9 - - - +
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Residues in contact with GLY 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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317B LEU 2.9 17.4 + - - -
318B LEU* 5.2 0.2 - - - -
320B TYR* 1.3 75.0 - - - +
322B VAL* 1.3 64.0 + - - +
323B HIS 3.2 3.3 + - - -
324B GLU* 3.3 6.4 + - - +
325B ILE* 3.0 31.7 + - - +
391B ILE* 4.8 3.4 - - - -
392B ILE* 5.4 3.1 - - - -
397B ARG* 3.4 23.5 - - - +
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B VAL* 3.7 44.9 - - + +
296B ILE* 3.8 25.8 - - + +
297B THR* 5.1 2.9 - - - +
318B LEU* 2.9 25.7 + - + +
319B LYS* 5.1 4.9 - - - +
320B TYR 3.5 0.2 - - - -
321B GLY* 1.3 77.7 - - - +
323B HIS* 1.3 82.7 + - + +
325B ILE* 3.6 5.5 + - - -
326B ILE* 3.3 27.1 + - + +
476B LEU* 4.9 8.5 - - + -
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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