Contacts of the helix formed by residues 298 - 314 (chain B) in PDB entry 5NC5
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 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU 4.5 5.5 + - - +
31B PRO* 5.2 0.7 - - + -
32B VAL* 3.4 32.2 - - - +
293B LEU* 4.2 0.9 - - - -
297B ALA* 1.3 71.8 - - - +
299B ALA* 1.3 56.7 + - - +
300B LEU* 2.6 39.2 + - - +
301B ASP* 2.7 38.9 + - + +
302B THR* 2.7 36.2 + - - -
1117B D10 4.1 17.2 - - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 3.0 24.1 + - + +
33B ALA* 4.5 6.3 - - - -
34B GLN 5.3 1.8 - - - +
137B LEU* 3.8 21.3 - - + +
293B LEU* 4.0 17.4 - - + +
297B ALA 4.0 1.2 - - - -
298B ASN* 1.3 70.0 + - - +
300B LEU* 1.3 70.3 + - + +
302B THR* 4.1 0.2 - - - -
303B ALA* 3.1 19.4 + - - +
329B THR* 5.4 2.5 - - - +
330B THR* 3.4 14.4 + - - +
333B VAL* 5.5 6.1 - - + -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 4.0 27.4 - - + -
298B ASN* 2.6 16.3 + - - +
299B ALA* 1.3 73.2 - - + +
301B ASP* 1.3 63.2 + - - +
303B ALA* 3.6 2.3 + - - +
304B ALA* 3.2 22.0 + - - +
330B THR* 4.0 32.0 - - + +
333B VAL* 4.0 19.7 - - + -
334B LYS* 4.1 15.5 - - + +
337B ILE* 4.6 14.8 - - + -
1117B D10 5.4 7.2 - - + -
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ASN* 2.7 44.3 + - + +
300B LEU* 1.3 76.4 - - - +
302B THR* 1.3 57.7 + - - +
304B ALA* 3.2 7.3 + - - +
305B ALA* 2.9 29.3 + - - +
1117B D10 5.9 0.5 - - - +
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Residues in contact with THR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.9 16.8 - - + -
170B SER 3.5 20.8 + - - +
171B GLY* 3.6 33.4 - - - +
172B VAL* 3.7 15.0 - - + +
293B LEU* 3.6 12.2 - - + +
297B ALA* 4.2 1.9 - - - +
298B ASN 2.7 18.2 + - - -
299B ALA 4.1 2.0 - - - -
301B ASP* 1.3 73.3 - - - +
303B ALA* 1.3 62.3 + - - +
305B ALA* 3.0 3.4 + - - +
306B ILE* 2.8 29.9 + - + +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 4.1 10.6 - - + +
138B MET* 4.3 15.0 - - - +
299B ALA 3.1 9.7 + - - +
300B LEU 4.1 2.7 - - - +
302B THR* 1.3 76.2 - - - +
304B ALA* 1.3 62.6 + - - +
306B ILE* 3.4 6.2 + - - +
307B ARG* 3.1 31.1 + - - +
328B ASP* 4.5 4.9 - - - +
330B THR* 3.3 36.8 - - + +
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Residues in contact with ALA 304 (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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300B LEU 3.2 12.2 + - - +
301B ASP* 3.2 10.9 + - - +
302B THR 3.1 0.4 - - - -
303B ALA* 1.3 80.7 - - - +
305B ALA* 1.3 56.9 + - - +
307B ARG* 3.3 8.3 + - - +
308B ALA* 2.9 26.7 + - - +
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Residues in contact with ALA 305 (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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169B THR* 3.7 20.8 - - + +
170B SER* 4.5 10.1 - - - +
301B ASP 2.9 16.1 + - - +
302B THR* 3.0 8.0 + - - +
304B ALA* 1.3 74.7 - - - +
306B ILE* 1.3 59.3 + - - +
308B ALA* 3.1 9.0 + - - +
309B GLU* 2.9 30.0 + - - +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.9 17.9 - - + -
138B MET* 3.7 22.9 - - + -
166B ILE* 4.3 12.9 - - + +
169B THR* 4.5 6.1 - - + -
172B VAL* 4.2 14.6 - - + -
291B ILE* 3.6 42.6 - - + -
302B THR* 2.8 25.3 + - + +
303B ALA* 3.7 4.5 - - - +
305B ALA* 1.3 78.3 - - - +
307B ARG* 1.3 57.5 + - - +
309B GLU* 3.4 4.9 + - - +
310B LEU* 3.0 45.6 + - + +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B MET* 4.6 6.6 - - + +
303B ALA* 3.1 26.1 + - - +
304B ALA* 3.6 7.0 - - - +
306B ILE* 1.3 76.3 - - - +
308B ALA* 1.3 58.6 + - - +
310B LEU* 3.4 7.5 + - - +
311B ALA* 2.9 29.5 + - - +
325B TYR* 3.3 61.7 + - + +
328B ASP* 2.7 29.9 + - - +
330B THR* 5.7 2.0 - - - +
331B PRO* 5.9 1.0 - - - +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ALA 2.9 15.5 + - - +
305B ALA* 3.1 13.0 + - - +
307B ARG* 1.3 77.6 - - - +
309B GLU* 1.3 62.2 + - - +
311B ALA* 3.0 20.9 + - - +
312B LYS* 3.2 13.0 + - - +
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Residues in contact with GLU 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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165B ALA* 3.9 12.1 - - - +
166B ILE* 4.4 9.2 - - + -
169B THR* 3.9 25.4 - - + +
305B ALA 2.9 15.2 + - - +
306B ILE 4.0 3.4 - - - +
308B ALA* 1.3 76.3 - - - +
310B LEU* 1.3 62.6 + - - +
312B LYS* 3.3 45.6 + - - +
313B MET* 3.2 27.6 + - - +
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Residues in contact with LEU 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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140B VAL* 4.1 17.5 - - + -
162B MET* 3.8 29.2 - - + -
166B ILE* 4.2 15.7 - - + -
289B LEU* 5.5 0.9 - - + -
306B ILE* 3.0 40.7 + - + +
307B ARG* 3.7 3.4 - - - +
309B GLU* 1.3 76.1 - - - +
311B ALA* 1.3 63.9 + - - +
313B MET* 3.1 18.9 + - - +
314B GLU* 3.3 17.1 + - - +
317B PHE* 4.4 3.9 - - + -
323B ILE* 4.4 13.2 - - + -
325B TYR* 3.4 37.2 - - + +
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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
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307B ARG 2.9 14.9 + - - +
308B ALA* 3.0 14.1 + - - +
310B LEU* 1.3 77.0 - - - +
312B LYS* 1.3 60.7 + - - +
314B GLU* 3.3 27.3 - - - +
315B PRO* 3.6 4.2 - - - +
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Residues in contact with LYS 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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308B ALA 3.2 9.1 + - - +
309B GLU* 3.3 42.8 + - - +
311B ALA* 1.3 79.7 - - + +
313B MET* 1.3 60.0 + - + +
315B PRO* 3.1 18.7 - - - +
316B PHE* 3.7 11.8 - - - -
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Residues in contact with MET 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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157B TYR* 4.9 0.6 + - - +
161B ASN 4.0 8.5 - - - +
162B MET* 3.8 34.3 - - - +
165B ALA* 3.4 24.9 - - + -
166B ILE* 4.1 19.1 - - + -
309B GLU* 3.2 33.8 + - - +
310B LEU* 3.1 15.5 + - - +
312B LYS* 1.3 76.3 - - + +
314B GLU* 1.3 64.3 + - - +
315B PRO* 3.2 4.7 - - - -
316B PHE* 3.0 21.6 + - - +
317B PHE* 3.3 22.8 + - + -
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Residues in contact with GLU 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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310B LEU* 3.3 14.6 + - - +
311B ALA* 3.3 19.2 - - - +
313B MET* 1.3 76.5 - - - +
315B PRO* 1.3 63.5 - - + +
316B PHE 3.2 0.9 + - - -
317B PHE* 3.4 42.9 + - + +
321B LEU 5.1 0.3 - - - +
322B LYS* 4.8 5.4 - - - +
323B ILE* 3.7 22.2 + - - +
325B TYR* 5.6 0.9 + - - -
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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