Contacts of the helix formed by residues 270 - 281 (chain I) in PDB entry 6C6S
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 THR 270 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268I ARG* 3.7 36.8 - - + +
269I ILE* 1.3 78.5 - - - +
271I ALA* 1.3 59.9 + - - +
272I ARG* 3.3 15.9 - - - +
273I HIS* 3.0 43.5 + - + +
274I ILE* 3.1 27.6 + - - +
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Residues in contact with ALA 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247I ARG* 6.1 2.5 - - - +
270I THR* 1.3 71.6 - - - +
272I ARG* 1.3 60.4 + - - +
274I ILE* 3.8 14.2 - - + +
275I ARG* 2.9 53.8 + - - +
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Residues in contact with ARG 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I THR* 3.2 15.6 + - - +
271I ALA* 1.3 78.0 - - - +
273I HIS* 1.3 61.9 + - + +
275I ARG* 3.3 10.2 + - - +
276I GLN* 2.9 44.7 + - - +
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Residues in contact with HIS 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I TYR 5.3 4.1 + - - -
263I VAL* 3.5 39.5 - - + +
267I ARG* 5.6 4.0 - - + -
268I ARG 3.8 16.5 + - - -
269I ILE* 3.9 8.2 - - + -
270I THR* 3.0 37.7 + - + +
272I ARG* 1.3 77.9 - - + +
274I ILE* 1.3 60.6 + - - +
276I GLN* 3.3 18.6 + - - +
277I LEU* 2.9 36.8 + - - +
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Residues in contact with ILE 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243I PRO* 3.3 36.1 - - + +
244I GLU* 4.4 8.1 - - - +
246I LEU* 4.2 18.8 - - + +
247I ARG* 4.3 21.3 - - + +
269I ILE* 3.9 12.6 - - + +
270I THR 3.1 15.4 + - - +
271I ALA* 3.8 14.6 - - + +
272I ARG 3.3 0.2 - - - -
273I HIS* 1.3 76.6 - - - +
275I ARG* 1.3 56.8 + - + +
277I LEU* 3.3 2.6 + - - +
278I GLU* 2.9 53.4 + - - +
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Residues in contact with ARG 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271I ALA* 2.9 48.4 + - - +
272I ARG* 3.7 9.2 - - - +
274I ILE* 1.3 77.8 - - + +
276I GLN* 1.3 56.9 + - + +
278I GLU* 3.7 10.7 - - - +
279I LYS* 2.8 33.1 + - - +
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Residues in contact with GLN 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260I LYS* 5.6 3.3 + - - -
262I TYR* 5.4 7.2 - - + +
272I ARG* 2.9 32.7 + - - +
273I HIS* 3.8 20.3 - - - +
274I ILE 3.3 0.2 - - - -
275I ARG* 1.3 76.4 - - + +
277I LEU* 1.3 60.7 + - + +
279I LYS* 3.8 17.2 - - - +
280I ASP* 2.9 43.0 + - - +
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Residues in contact with LEU 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241I LEU* 6.2 0.4 - - + -
243I PRO* 3.7 20.4 - - + +
246I LEU* 3.8 29.4 - - + -
255I ILE* 4.6 15.0 - - + -
262I TYR* 3.5 40.6 - - + -
263I VAL* 4.9 7.6 - - + -
273I HIS* 2.9 24.5 + - + +
274I ILE 3.8 1.1 - - - +
276I GLN* 1.3 79.3 - - + +
278I GLU* 1.3 57.9 + - - +
280I ASP 3.5 0.5 + - - -
281I ASP 3.1 21.5 + - - -
282I VAL* 3.2 37.6 + - + +
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Residues in contact with GLU 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242I VAL* 5.4 1.2 - - - +
243I PRO* 3.7 19.1 - - + +
244I GLU* 4.1 21.7 + - - +
274I ILE* 2.9 40.9 + - - +
275I ARG* 3.7 9.9 - - - +
277I LEU* 1.3 75.7 - - - +
279I LYS* 1.3 59.7 + - - +
281I ASP* 4.0 8.6 + - - +
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Residues in contact with LYS 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275I ARG 2.8 16.1 + - - +
276I GLN* 3.8 20.8 - - - +
277I LEU 3.2 0.2 - - - -
278I GLU* 1.3 76.8 - - - +
280I ASP* 1.3 75.2 + - - +
281I ASP* 3.2 7.8 + - - +
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Residues in contact with ASP 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I LYS* 4.7 5.6 + - - -
262I TYR* 3.5 24.7 + - + +
276I GLN* 2.9 25.9 + - - +
279I LYS* 1.3 93.8 + - - +
281I ASP* 1.3 69.6 + - - +
282I VAL* 3.7 18.2 - - + +
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Residues in contact with ASP 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277I LEU 3.1 6.4 + - - -
278I GLU* 4.0 6.9 + - - +
279I LYS 3.2 6.3 - - - +
280I ASP* 1.3 81.3 - - - +
282I VAL* 1.3 59.1 + - - +
283I LYS* 3.3 33.6 + - - +
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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