Contacts of the helix formed by residues 299 - 309 (chain B) in PDB entry 6CP3
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 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B TYR* 2.4 39.9 + - - -
284B SER* 5.2 0.5 + - - -
289B ARG* 5.0 4.5 + - - -
297B PRO* 3.7 10.2 - - - +
298B GLY* 1.3 71.8 + - - +
300B VAL* 1.3 59.0 + - - +
301B PHE 3.1 3.6 - - - -
302B TYR* 2.9 28.1 + - + +
303B LEU* 3.2 10.2 + - - +
267F GLU* 3.3 31.8 - - + +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 4.0 27.6 - - + -
280B TYR* 4.1 19.3 - - + -
296B TYR* 3.7 17.5 - - + -
297B PRO* 2.9 21.3 + - + +
298B GLY 3.4 1.0 - - - -
299B ASP* 1.3 76.0 + - - +
301B PHE* 1.3 65.4 + - - +
302B TYR 3.3 0.2 - - - -
303B LEU* 3.7 10.2 + - + +
304B HIS* 3.3 23.3 + - + -
339B TYR* 3.6 27.6 - - + -
340B ILE* 4.0 12.1 - - + -
343B ASN* 4.4 2.6 + - - +
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Residues in contact with PHE 301 (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 ASP* 3.1 0.6 - - - +
300B VAL* 1.3 82.6 - - - +
302B TYR* 1.3 58.9 + - - +
304B HIS* 3.5 3.3 + - - +
305B SER* 3.0 27.4 + - - -
339B TYR* 4.8 0.2 + - - -
343B ASN* 3.3 36.1 - - + +
346B SER* 3.6 15.3 - - - -
347B ILE* 4.1 22.0 - - + -
222F MET* 4.5 22.0 - - + -
229F ARG* 4.0 19.1 - - - -
260F ARG* 3.2 52.9 - - - -
263F GLN* 3.4 31.0 - - - +
267F GLU* 5.1 0.4 - - - -
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP* 2.9 18.9 + - + +
301B PHE* 1.3 83.4 - - - +
303B LEU* 1.3 57.8 + - - +
305B SER* 3.3 4.8 - - - -
306B ARG* 2.9 73.8 + - + +
68F GLU* 5.7 0.5 + - - -
222F MET 4.0 10.3 - - - -
223F ASN 3.9 11.5 + - - -
224F GLU 3.2 23.3 - - - -
225F PRO* 3.6 26.0 - - + +
226F PRO* 5.1 5.8 - - + -
229F ARG* 3.5 18.4 - - - +
267F GLU* 3.7 20.3 + - - +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 3.8 15.0 - - + -
250B PHE* 3.6 28.1 - - + -
276B GLN* 3.4 32.8 - - + +
280B TYR* 4.0 37.0 - - + -
299B ASP 3.2 10.3 + - - +
300B VAL* 3.9 13.0 - - + +
301B PHE 3.2 0.6 - - - -
302B TYR* 1.3 80.4 - - - +
304B HIS* 1.3 68.2 + - + +
306B ARG* 3.4 16.1 + - - +
307B LEU* 3.0 27.3 + - + +
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Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 3.5 51.2 + - + +
276B GLN* 4.4 8.3 + - - -
277B ALA* 3.7 28.0 + - + -
300B VAL* 3.3 26.3 + - + +
301B PHE* 3.5 4.3 + - - +
303B LEU* 1.3 85.3 - - + +
305B SER* 1.3 56.8 + - - +
307B LEU* 3.8 5.8 - - - -
308B LEU* 3.0 35.1 + - + +
329B ILE* 5.1 0.2 - - - +
340B ILE* 4.6 12.0 - - + +
343B ASN* 5.4 5.4 - - + +
344B VAL* 4.2 19.8 - - + +
347B ILE* 3.6 16.0 - - + +
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Residues in contact with SER 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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301B PHE* 3.0 22.8 + - - -
302B TYR* 3.3 10.1 - - - -
304B HIS* 1.3 76.9 - - - +
306B ARG* 1.3 57.5 + - - +
307B LEU 3.1 0.3 + - - -
309B GLU* 2.9 34.0 + - - +
347B ILE* 3.5 11.1 - - - +
222F MET* 2.3 55.4 + - - +
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Residues in contact with ARG 306 (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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52B GLU* 5.6 1.6 + - - -
132B GLN* 2.7 36.2 + - - +
133B VAL 5.2 11.2 - - - +
246B TYR* 4.1 13.1 + - - -
250B PHE* 3.4 24.4 - - - -
302B TYR* 2.9 61.8 + - + +
303B LEU* 3.7 23.6 - - - +
305B SER* 1.3 73.8 + - - +
307B LEU* 1.3 61.5 + - - +
309B GLU* 4.4 4.7 - - - +
310B ARG* 3.8 19.4 + - - +
68F GLU* 4.4 10.3 + - - -
222F MET 5.0 0.7 - - - -
223F ASN* 4.6 12.1 - - + +
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Residues in contact with LEU 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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249B PRO* 3.7 19.7 - - + +
250B PHE* 3.5 29.1 - - + +
253B ALA* 4.2 4.3 - - + +
270B TYR* 3.5 44.8 + - + +
273B LEU* 3.8 28.0 - - + -
276B GLN* 3.8 16.6 - - - +
303B LEU 3.0 17.8 + - - +
304B HIS* 3.8 5.6 - - + +
306B ARG* 1.3 78.6 - - - +
308B LEU* 1.3 68.2 + - + +
309B GLU 3.3 0.7 + - - -
310B ARG* 3.3 17.7 + - - +
311B ALA* 5.7 0.2 - - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 3.2 26.7 - - + -
270B TYR* 3.8 29.6 - - + -
273B LEU* 4.7 5.2 - - + -
304B HIS* 3.0 24.2 + - + +
307B LEU* 1.3 80.7 - - + +
309B GLU* 1.3 61.9 + - - +
310B ARG 3.2 1.2 + - - -
311B ALA* 3.5 10.3 + - - +
325B ALA* 3.9 16.4 - - + -
327B PRO* 3.8 21.8 - - + -
344B VAL* 4.5 8.3 - - + -
347B ILE* 3.9 21.1 - - + -
348B THR* 3.7 28.5 - - + -
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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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135B ALA* 3.3 24.7 - - + +
136B PRO* 4.1 0.5 - - - +
141B ARG* 3.4 23.0 + - - -
166B ARG* 2.4 32.7 + - - +
305B SER 2.9 19.4 + - - +
306B ARG* 5.0 2.7 - - - -
307B LEU 3.2 0.2 - - - -
308B LEU* 1.3 76.8 - - - +
310B ARG* 1.3 57.5 + - - +
311B ALA 3.1 7.3 + - - +
347B ILE* 5.3 0.7 - - + -
190F ARG* 4.4 1.4 - - - +
191F THR* 3.4 34.0 + - - -
222F MET* 3.7 30.0 - - + +
223F ASN* 4.4 9.1 - - + +
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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