Contacts of the helix formed by residues 295 - 309 (chain B) in PDB entry 6UPR
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 ARG 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B ASN* 5.4 1.6 - - - -
213B GLN* 6.3 0.8 - - - +
291B GLN* 2.9 38.3 + - - +
293B HIS 3.3 0.6 - - - -
294B SER* 1.3 80.3 - - - +
296B HIS* 1.3 92.3 + - - +
297B TYR 3.5 0.7 - - - -
298B GLU* 3.6 2.1 + - - +
299B LEU* 3.1 24.3 + - - +
302B ARG* 4.6 3.9 + - - +
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Residues in contact with HIS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 4.1 8.2 - - + -
176B ASP 3.7 22.4 - - - -
177B SER* 3.6 18.6 + - - +
178B LYS* 3.4 21.8 - - - +
179B VAL* 3.2 28.2 + - - -
180B ASN* 3.1 32.6 + - - -
291B GLN 3.4 4.5 + - - -
292B THR* 3.7 13.9 - - + +
295B ARG* 1.3 99.2 - - - +
297B TYR* 1.3 62.9 + - - +
299B LEU* 3.4 6.0 + - - +
300B TYR* 3.1 20.8 + - - +
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Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 3.6 53.3 - + + -
131B TYR* 3.3 16.6 - + - -
132B LEU* 3.2 32.2 - - + +
135B GLU* 3.0 32.8 + - - -
149B ARG* 3.4 23.1 - - - +
292B THR 2.8 21.4 + - - +
293B HIS* 3.5 16.8 - + - +
296B HIS* 1.3 73.5 - - - +
298B GLU* 1.3 59.2 + - - +
300B TYR* 3.2 5.7 + + - +
301B ARG* 2.7 48.8 + - + +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 5.6 0.2 - - - +
293B HIS* 3.4 30.5 + - - +
294B SER* 3.4 24.9 - - - +
295B ARG 3.6 2.0 + - - +
296B HIS 3.3 0.6 - - - -
297B TYR* 1.3 82.7 - - - +
299B LEU* 1.3 56.9 + - - +
301B ARG* 3.3 38.7 + - - +
302B ARG* 2.9 49.8 + - - +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B SER* 3.5 40.2 - - - +
178B LYS* 6.0 0.7 - - + -
295B ARG 3.1 17.9 + - - +
296B HIS* 3.7 3.8 - - - +
297B TYR 3.2 0.2 - - - -
298B GLU* 1.3 73.9 - - - +
300B TYR* 1.3 64.5 + - - +
302B ARG* 3.2 29.2 + - + +
303B CYS* 3.3 21.0 + - + +
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP* 3.6 39.9 + - + +
128B PHE* 3.4 48.7 - + + -
129B GLU* 2.7 35.7 + - - +
132B LEU* 4.4 5.2 - - + -
178B LYS* 4.6 7.6 - - - +
296B HIS 3.1 14.4 + - - +
297B TYR* 3.5 11.4 - + - +
299B LEU* 1.3 76.2 - - - +
301B ARG* 1.3 62.7 + - - +
303B CYS* 3.2 9.7 + - + +
304B LYS* 2.9 54.7 + - + +
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.9 13.1 - - + +
135B GLU* 3.6 23.3 + - - -
297B TYR* 2.7 36.5 + - + +
298B GLU* 3.3 32.1 + - - +
299B LEU 3.2 0.2 - - - -
300B TYR* 1.3 79.8 - - - +
302B ARG* 1.3 70.8 + - - +
304B LYS* 3.9 2.6 - - - -
305B LEU* 2.9 58.2 + - + +
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Residues in contact with ARG 302 (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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294B SER 5.2 2.2 + - - -
295B ARG* 4.6 3.8 + - - +
298B GLU* 2.9 36.3 + - - +
299B LEU* 3.2 52.3 - - + +
300B TYR 3.3 0.2 - - - -
301B ARG* 1.3 81.0 - - - +
303B CYS* 1.3 62.8 + - - +
305B LEU* 4.3 3.7 - - - +
306B GLU* 3.2 35.0 + - + +
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Residues in contact with CYS 303 (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 LEU* 3.3 10.3 + - + +
300B TYR* 3.2 13.6 + - + +
302B ARG* 1.3 80.6 - - - +
304B LYS* 1.3 60.2 + - - +
306B GLU* 4.0 3.4 - - - +
307B GLU* 3.0 38.9 + - - +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 3.6 22.9 + - - +
132B LEU* 3.6 20.2 - - + -
300B TYR* 2.9 44.6 + - + +
301B ARG 4.0 0.4 - - - +
303B CYS* 1.3 80.3 - - - +
305B LEU* 1.3 51.2 + - - +
307B GLU* 2.5 40.0 + - - +
308B MET* 2.7 55.2 + - + +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.9 25.6 - - + -
136B LEU* 4.3 11.4 - - + -
301B ARG* 2.9 62.2 + - + +
302B ARG* 4.3 2.9 - - - +
304B LYS* 1.3 75.8 - - - +
306B GLU* 1.3 60.5 + - + +
308B MET* 3.2 9.7 + - - -
309B GLY 3.0 8.0 + - - -
310B PHE* 2.9 58.4 + - + -
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Residues in contact with GLU 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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302B ARG* 3.2 21.8 + - + +
303B CYS* 4.2 3.0 - - - +
305B LEU* 1.3 75.3 - - + +
307B GLU* 1.3 65.8 + - - +
309B GLY* 3.2 12.3 + - - -
310B PHE 3.9 15.6 - - - +
311B GLN* 5.7 4.0 - - - -
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B CYS* 3.0 29.3 + - - +
304B LYS* 2.5 42.7 + - - +
306B GLU* 1.3 77.3 - - - +
308B MET* 1.3 60.1 + - + +
309B GLY* 3.4 0.9 + - - -
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 4.6 4.5 - - - +
132B LEU* 4.2 8.3 - - + -
133B GLN* 4.0 23.8 - - - +
136B LEU* 3.9 20.4 - - + -
304B LYS* 2.7 46.7 + - + +
305B LEU* 3.6 13.2 - - - +
306B GLU 3.2 0.6 - - - -
307B GLU* 1.3 74.0 - - + +
309B GLY* 1.3 57.2 + - - +
310B PHE* 3.7 27.0 - - + -
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Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU 3.0 2.4 + - - -
306B GLU 3.2 11.3 + - - -
307B GLU 3.2 1.3 - - - -
308B MET* 1.3 79.0 - - - +
310B PHE* 1.3 66.9 + - - +
311B GLN* 3.7 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