Contacts of the helix formed by residues 314 - 329 (chain B) in PDB entry 1N8T
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 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ARG* 4.3 2.6 - - - +
305B HIS* 3.6 4.2 + - - -
306B PHE* 2.9 37.9 + - - -
309B THR* 2.8 32.3 + - - -
310B PRO 3.2 4.9 + - - +
311B LEU* 2.9 17.3 + - - +
312B GLU 3.5 0.6 - - - -
313B LYS* 1.3 73.7 - - - +
315B ALA* 1.3 66.6 + - - +
316B PRO* 3.0 27.8 - - - +
317B VAL* 2.9 20.0 + - + +
318B LEU* 2.8 26.6 + - - +
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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
----------------------------------------------------------
41B LEU* 3.6 19.1 - - + +
43B LEU* 4.1 13.0 - - + -
52B LEU* 4.2 10.9 - - + +
302B MET* 4.8 1.1 - - - -
305B HIS* 3.1 18.5 - - + +
313B LYS 3.5 3.2 + - - -
314B ASN* 1.3 68.6 - - - +
316B PRO* 1.3 74.5 - - + +
318B LEU* 3.3 2.7 + - - +
319B LEU* 2.9 29.7 + - - +
492B MET* 4.3 17.9 - - + -
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Residues in contact with PRO 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET* 4.4 7.9 - - - -
305B HIS* 3.8 8.3 - - - +
306B PHE* 4.0 15.0 - - + -
314B ASN* 3.0 22.2 - - - +
315B ALA* 1.3 91.1 - - + +
317B VAL* 1.3 61.4 + - - +
319B LEU* 3.4 6.0 + - + +
320B ALA* 3.0 23.0 + - - +
492B MET* 3.9 23.6 - - + +
495B HIS* 3.7 35.4 - - + +
496B LYS* 3.8 6.2 - - - -
499B VAL* 4.8 0.9 - - - -
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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
----------------------------------------------------------
68B LEU* 4.6 7.0 - - + -
71B ALA* 5.7 2.2 - - + -
76B VAL* 4.7 4.9 - - + -
306B PHE* 3.5 23.3 - - + -
311B LEU* 3.4 48.7 - - + +
314B ASN* 2.9 27.3 + - + +
316B PRO* 1.3 74.6 - - - +
318B LEU* 1.3 69.5 + - - +
320B ALA* 3.1 2.5 + - - +
321B MET* 2.9 32.7 + - + +
499B VAL* 3.8 20.4 - - + -
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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
----------------------------------------------------------
41B LEU* 4.3 11.2 - - + -
52B LEU* 4.7 8.3 - - + -
54B TYR* 4.2 23.6 - - + +
64B MET* 3.7 25.8 - - + -
68B LEU* 4.0 24.0 - - + -
311B LEU 4.1 0.4 - - - +
312B GLU 3.1 28.0 - - - +
313B LYS* 3.9 3.4 - - - -
314B ASN 2.8 36.4 + - - +
315B ALA* 3.7 4.3 - - - +
317B VAL* 1.3 74.1 - - - +
319B LEU* 1.3 64.1 + - - +
321B MET* 3.4 3.7 + - + +
322B LEU* 3.1 33.7 + - + +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.1 22.7 - - + -
315B ALA 2.9 17.8 + - - +
316B PRO* 3.6 5.6 - - + +
318B LEU* 1.3 77.8 - - - +
320B ALA* 1.3 62.3 + - - +
322B LEU* 3.3 7.3 + - + +
323B GLY 3.1 16.8 + - - -
404B ASP* 4.8 6.1 - - - +
474B ASN* 3.5 31.5 - - + +
476B ILE* 4.8 4.9 - - + -
492B MET* 3.7 42.2 - - + -
493B TYR* 4.4 18.4 - - + -
496B LYS* 4.0 23.1 + - + +
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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
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316B PRO 3.0 15.9 + - - +
317B VAL 3.1 4.0 + - - +
319B LEU* 1.3 77.2 - - - +
321B MET* 1.3 59.5 + - - +
323B GLY 3.0 2.3 + - - -
324B ILE* 2.9 28.5 + - - +
496B LYS* 3.5 31.6 - - - +
499B VAL* 3.6 21.1 - - + -
500B GLN* 3.1 19.5 - - + +
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Residues in contact with MET 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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64B MET* 5.8 2.2 - - + -
67B LEU* 3.6 52.5 - - + +
68B LEU* 5.0 7.9 - - + -
70B LEU* 3.9 24.5 - - + -
71B ALA* 3.9 17.9 - - + +
317B VAL* 2.9 22.9 + - + +
318B LEU* 4.2 4.0 - - + +
320B ALA* 1.3 73.5 - - - +
322B LEU* 1.3 66.8 + - + +
324B ILE* 3.1 17.6 + - + +
325B TRP* 2.9 23.4 + - - +
499B VAL* 4.2 10.8 - - - -
503B VAL* 3.8 25.6 - - + -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 6.1 0.2 - - + -
54B TYR* 3.6 35.9 - - + -
57B ASN* 3.6 20.6 - - + +
59B VAL* 3.9 28.5 - - + -
64B MET* 4.0 18.4 - - + -
67B LEU* 4.8 1.8 - - + -
318B LEU* 3.1 26.8 + - + +
319B LEU* 3.6 8.1 - - + +
321B MET* 1.3 75.0 - - - +
323B GLY* 1.3 64.3 + - - +
325B TRP* 3.1 9.7 - - + +
326B TYR* 3.1 36.2 + - + +
474B ASN* 3.8 14.1 - - - +
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Residues in contact with GLY 323 (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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319B LEU 3.1 9.8 + - - -
320B ALA 3.0 8.2 + - - -
322B LEU* 1.3 74.5 - - - +
324B ILE* 1.3 57.4 + - - +
326B TYR* 3.0 7.8 + - - +
327B ILE* 2.8 39.5 + - - +
335B GLN* 5.0 13.2 - - - -
496B LYS* 5.2 1.8 - - - -
500B GLN* 3.6 14.1 - - - -
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Residues in contact with ILE 324 (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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3B LEU* 5.6 0.2 - - + -
9B PHE* 5.4 2.9 - - + -
12B LEU* 5.5 4.0 - - + -
67B LEU* 4.9 3.4 - - + -
70B LEU* 4.3 22.2 - - + -
320B ALA 2.9 22.6 + - - +
321B MET* 3.1 26.7 + - + +
323B GLY* 1.3 72.2 - - - +
325B TRP* 1.3 59.1 + - - +
327B ILE* 4.5 2.0 - - - -
328B ASN* 2.7 48.1 + - + +
329B CYS* 3.7 0.9 + - - -
500B GLN* 3.7 13.4 + - + -
503B VAL* 3.9 19.1 - - + -
504B TRP* 3.6 36.6 - - + +
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Residues in contact with TRP 325 (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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12B LEU* 3.6 42.4 - - + -
15B TRP* 3.9 24.2 - + - -
16B HIS* 3.9 20.4 - + + -
23B LEU* 4.7 2.9 - - + -
58B LEU 2.8 29.5 + - - -
59B VAL* 4.0 11.6 - - + +
63B VAL* 3.7 23.1 - - + -
67B LEU* 4.2 10.8 - - + -
321B MET 2.9 11.8 + - - +
322B LEU* 3.1 11.9 - - - +
323B GLY 3.1 0.2 - - - -
324B ILE* 1.3 78.4 - - - +
326B TYR* 1.3 82.2 + + - +
329B CYS* 3.1 38.7 + - + +
330B PHE* 3.1 32.0 + + - -
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Residues in contact with TYR 326 (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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57B ASN* 2.5 36.2 + - - +
58B LEU* 3.0 27.4 + - + -
322B LEU* 3.1 28.7 + - + -
323B GLY* 3.0 8.7 + - - +
325B TRP* 1.3 96.2 - + - +
327B ILE* 1.3 54.9 + - + +
330B PHE* 3.4 25.7 - + - +
331B GLY 2.9 10.0 + - - -
332B CYS* 2.8 33.8 + - + -
335B GLN* 5.7 0.9 - - - -
400B MET* 4.3 7.9 - - - -
402B PRO* 3.8 37.2 - - + -
472B PRO* 3.2 20.0 - - + +
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Residues in contact with ILE 327 (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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399A LYS* 5.0 1.8 - - - +
323B GLY* 2.8 25.5 + - - +
324B ILE 4.0 0.7 - - - +
326B TYR* 1.3 78.7 - - + +
328B ASN* 1.3 79.4 + - - +
331B GLY* 3.2 23.9 + - - -
332B CYS* 3.9 20.0 - - + +
334B THR 5.9 0.9 - - - +
335B GLN* 6.1 1.8 - - - +
373B GLN* 3.8 18.3 - - + +
374B THR 3.7 17.9 - - - +
376B PRO* 3.8 38.8 - - + -
500B GLN* 4.2 5.4 - - - +
504B TRP* 3.9 17.3 - - + -
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Residues in contact with ASN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.2 7.1 - - - +
9B PHE* 3.9 20.0 - - + -
13B GLN* 3.0 24.4 + - - -
324B ILE* 2.7 38.1 + - + +
327B ILE* 1.3 78.4 - - - +
329B CYS* 1.3 59.6 + - - +
331B GLY* 4.7 0.7 - - - -
372B HIS* 4.1 9.5 + - - +
373B GLN* 3.0 37.7 + - - +
504B TRP* 2.8 24.0 + - - +
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Residues in contact with CYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 5.3 0.2 - - - -
12B LEU* 3.0 42.2 - - - -
13B GLN* 4.0 18.4 - - - +
16B HIS* 3.2 36.4 + - + -
324B ILE 4.9 0.2 - - - -
325B TRP* 3.1 28.4 + - + +
327B ILE 3.4 0.2 - - - -
328B ASN* 1.3 87.0 - - - +
330B PHE* 1.3 62.3 + - - +
331B GLY* 3.2 2.1 + - - -
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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
------------------------------------------------------------
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