Contacts of the helix formed by residues 297 - 311 (chain B) in PDB entry 7UUT
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 GLY 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PRO* 4.0 8.7 - - - -
86B ALA* 3.5 22.1 - - - +
90B TRP* 4.4 2.3 - - - -
100B HIS* 3.0 28.0 + - - -
295B CYS 3.6 1.4 + - - -
296B PRO* 1.3 75.7 - - - +
298B GLY* 1.3 63.2 + - - -
301B ARG* 3.4 18.4 + - - +
302B MET* 4.9 0.2 - - - -
96D GLN* 4.7 1.0 - - - +
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO* 3.6 10.7 - - - +
86B ALA 3.4 11.7 + - - -
88B PRO* 4.5 0.6 - - - +
90B TRP* 3.7 11.4 - - - -
131B MET 3.6 2.2 - - - -
132B ASN* 3.5 20.4 - - - -
297B GLY* 1.3 76.1 - - - +
299B ARG* 1.3 65.9 + - - -
300B LEU 3.4 1.6 - - - -
302B MET* 3.3 22.9 + - - +
96D GLN* 4.1 0.4 - - - -
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP* 2.8 44.9 + - - +
75B PHE* 3.8 8.9 - - - -
130B ASP 3.1 23.5 + - - -
131B MET 2.8 24.0 + - - +
132B ASN* 4.0 0.2 - - - +
133B LEU 3.0 30.9 + - - +
134B ALA* 4.1 0.2 - - - +
135B HIS* 4.6 11.9 + - - -
298B GLY* 1.3 72.1 - - - -
300B LEU* 1.3 59.8 + - - +
302B MET* 3.2 5.0 + - - +
303B GLU* 2.8 63.0 + - + +
93D SER* 6.3 3.3 - - - -
96D GLN* 3.6 7.0 + - - +
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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
----------------------------------------------------------
299B ARG* 1.3 77.7 - - - +
301B ARG* 1.3 62.2 + - - +
303B GLU* 3.2 17.6 + - + +
304B ARG* 3.0 58.0 + - + +
93D SER* 4.3 14.8 - - - +
96D GLN* 3.0 42.9 + - + +
97D ARG* 3.5 32.8 - - + -
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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
----------------------------------------------------------
100B HIS* 5.8 0.7 - - + -
153B THR* 3.0 49.1 + - - +
156B PHE* 3.8 7.0 - - - +
157B HIS 3.5 7.5 - - - +
160B GLU* 2.8 41.1 + - - -
296B PRO* 3.7 28.5 - - + +
297B GLY 3.4 21.7 + - - +
298B GLY 3.6 2.1 + - - +
299B ARG 3.3 0.6 - - - -
300B LEU* 1.3 80.0 - - - +
302B MET* 1.3 70.2 + - + +
304B ARG* 3.4 7.1 + - - +
305B LEU* 3.1 43.6 + - + +
165C GLU* 5.7 0.6 + - - -
166C LEU* 4.4 9.5 + - - +
96D GLN* 4.4 0.4 + - - -
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Residues in contact with MET 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 3.8 19.1 - - + +
84B PRO* 3.7 41.5 - - + -
134B ALA* 3.7 16.4 - - + -
148B ILE* 3.7 36.3 - - + +
149B PRO* 3.9 8.5 - - - +
153B THR* 4.1 11.0 - - + -
296B PRO 4.4 2.7 - - - +
298B GLY 3.3 12.8 + - - +
299B ARG* 3.2 7.5 + - - +
301B ARG* 1.3 94.4 - - + +
303B GLU* 1.3 58.5 + - - +
305B LEU* 3.2 1.8 + - + +
306B ILE* 2.8 35.6 + - + +
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Residues in contact with GLU 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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134B ALA* 3.7 18.3 - - + +
135B HIS* 5.1 4.9 + - - +
299B ARG* 2.8 59.4 + - - +
300B LEU* 3.7 19.8 - - + +
302B MET* 1.3 75.0 - - - +
304B ARG* 1.3 58.0 + - + +
306B ILE* 3.4 8.3 + - + +
307B ASP* 3.1 32.6 + - - +
93D SER* 5.9 2.8 - - - -
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 3.0 50.8 + - + +
301B ARG* 3.9 7.4 - - - +
302B MET 3.2 0.2 - - - -
303B GLU* 1.3 76.2 - - + +
305B LEU* 1.3 61.4 + - + +
307B ASP* 3.3 4.5 + - - +
308B LEU* 3.1 28.2 + - - +
165C GLU* 3.7 29.2 + - - +
166C LEU 3.3 24.0 - - - +
167C GLY* 3.5 19.3 - - - +
168C ALA* 4.6 8.6 - - - +
237C ASP* 3.3 29.8 + - - +
257C LYS* 5.5 0.4 - - - +
97D ARG* 3.5 23.4 - - - +
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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
----------------------------------------------------------
148B ILE* 3.8 23.6 - - + -
152B MET* 3.8 14.7 - - + +
153B THR* 3.6 43.7 - - - +
156B PHE* 3.7 23.3 - - + -
301B ARG* 3.1 37.8 + - + +
302B MET* 3.9 1.1 - - + +
304B ARG* 1.3 77.7 - - + +
306B ILE* 1.3 65.3 + - - +
308B LEU* 3.2 16.4 + - + +
309B VAL* 3.2 26.8 + - - +
166C LEU* 4.9 4.7 - - + -
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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
----------------------------------------------------------
82B VAL* 3.7 25.4 - - + -
134B ALA* 4.0 15.3 - - + -
135B HIS 3.4 22.9 - - - +
136B LEU* 5.0 0.2 - - + -
137B PRO* 3.6 30.7 - - + -
140B ILE* 3.7 9.9 - - + +
148B ILE* 3.8 24.7 - - + -
302B MET 2.8 20.9 + - - +
303B GLU* 3.6 7.6 - - + +
305B LEU* 1.3 76.8 - - - +
307B ASP* 1.3 55.6 + - - +
309B VAL* 3.1 4.0 + - - +
310B PHE* 2.7 34.0 + - + +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU* 3.1 17.9 + - - +
304B ARG* 3.5 9.7 - - - +
305B LEU 3.2 0.2 - - - -
306B ILE* 1.3 81.3 - - - +
308B LEU* 1.3 59.1 + - - +
310B PHE* 4.1 7.3 - - - +
311B TYR* 2.9 58.2 + - + +
167C GLY 4.1 17.0 - - - +
169C THR* 4.6 9.7 + - - -
192C GLY* 4.6 4.4 - - - -
193C ARG* 5.5 0.9 + - - +
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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
----------------------------------------------------------
152B MET* 5.3 0.4 - - - -
156B PHE* 3.7 31.4 - - + -
188B LEU* 4.0 11.4 - - + -
304B ARG 3.1 11.0 + - - +
305B LEU* 3.5 25.4 - - + +
306B ILE 3.2 0.2 - - - -
307B ASP* 1.3 75.9 - - - +
309B VAL* 1.3 58.7 + - + +
312B LYS 3.3 1.4 + - - -
313B ARG* 2.7 57.9 + - + +
314B VAL* 3.4 7.4 + - + +
166C LEU* 4.3 4.9 - - + -
167C GLY* 3.7 18.6 - - - +
190C GLY* 3.3 24.2 - - - +
191C ALA 3.9 3.4 - - - +
192C GLY* 4.1 1.6 - - - -
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Residues in contact with VAL 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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140B ILE* 4.1 31.2 - - + -
141B PRO* 6.2 0.2 - - + -
144B ALA* 4.9 3.4 - - + +
148B ILE* 4.1 10.5 - - + -
152B MET* 3.8 28.3 - - + -
305B LEU 3.3 14.4 - - - +
306B ILE 3.1 6.1 + - - +
308B LEU* 1.3 76.6 - - + +
310B PHE* 1.3 66.0 + - - +
312B LYS* 3.1 16.3 + - - +
314B VAL* 3.7 18.4 - - + +
315B ASP* 5.5 1.3 - - - +
316B PRO* 4.0 13.9 - - + -
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Residues in contact with PHE 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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137B PRO* 4.3 19.7 - - + -
139B GLU* 3.8 39.7 - - + -
140B ILE* 4.3 10.3 - - + +
306B ILE* 2.7 23.0 + - + +
307B ASP* 3.8 10.8 - - - +
309B VAL* 1.3 75.3 - - - +
311B TYR* 1.3 97.2 + + - +
312B LYS* 3.3 16.1 + - - +
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Residues in contact with TYR 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 ASP* 2.9 46.1 + - + +
310B PHE* 1.3 104.8 - + - +
312B LYS* 1.3 70.4 + - - +
313B ARG* 3.3 19.5 + - + +
192C GLY 4.0 14.8 - - - +
193C ARG* 3.3 54.0 + - + -
213C THR* 3.7 34.6 - - + +
214C ASP* 4.8 1.8 - - - -
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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