Contacts of the strand formed by residues 239 - 249 (chain C) in PDB entry 4I7Z
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 239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C HIS* 5.3 2.0 - - - -
28C ALA* 3.5 17.0 - - - -
30C LYS* 3.4 9.0 - - - +
154C ASN* 3.4 8.7 - - - -
155C ARG* 2.7 50.7 + - - +
236C ASN* 5.3 0.4 - - - -
238C GLY* 1.3 74.6 - - - -
240C PHE* 1.3 58.0 + - - -
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Residues in contact with PHE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ARG 3.9 6.7 - - - -
20C ILE* 3.7 19.5 - - + -
22C CYS* 3.2 27.8 - - + -
23C ALA* 3.7 24.9 - - + -
26C HIS* 3.8 27.3 - - + +
28C ALA 3.3 7.7 + - - +
29C ALA* 3.4 9.5 - - - +
30C LYS 3.1 17.8 + - - +
152C GLY* 3.4 27.6 - - - -
153C ALA 2.9 22.0 - - - -
154C ASN* 3.5 4.5 - - + +
239C GLY* 1.3 73.0 - - - -
241C GLY* 1.3 58.5 + - - +
242C GLN* 3.3 41.7 - - + -
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Residues in contact with GLY 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS 3.2 16.4 + - - -
32C ALA* 3.4 13.8 - - - +
151C LEU 4.2 0.2 - - - +
152C GLY* 3.6 2.3 - - - -
153C ALA 2.8 42.9 + - - +
155C ARG* 4.4 0.2 - - - +
239C GLY 4.1 0.4 + - - -
240C PHE* 1.3 77.8 - - - +
242C GLN* 1.3 63.5 + - - -
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Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 4.6 6.7 - - - +
18C GLY 3.0 26.2 + - - -
19C ARG* 2.7 34.2 + - - +
20C ILE* 3.4 13.5 - - - +
23C ALA* 5.2 0.5 - - - +
32C ALA* 3.9 8.3 + - - +
151C LEU 3.3 9.6 - - - +
240C PHE* 3.3 29.3 - - + -
241C GLY* 1.3 73.2 - - - -
243C ASP* 1.3 65.0 + - - +
244C ASP* 5.1 7.4 + - - +
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Residues in contact with ASP 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA 3.3 17.9 - - - +
33C GLU* 3.4 13.6 - - - +
34C VAL* 2.9 36.7 + - + +
151C LEU* 2.8 34.9 + - + +
242C GLN* 1.3 78.4 - - - +
244C ASP* 1.3 82.1 + - - +
245C THR* 5.4 0.2 - - - -
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Residues in contact with ASP 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU* 3.9 17.6 - - - +
14C ARG* 4.4 3.3 + - - -
18C GLY 5.6 1.6 - - - +
148C ALA* 6.2 0.9 - - + -
149C ILE 3.3 7.9 - - - +
150C HIS* 2.4 40.4 + - + +
151C LEU 5.0 0.3 + - - +
242C GLN* 5.1 7.5 + - - +
243C ASP* 1.3 95.6 + - - +
245C THR* 1.3 66.0 + - - +
246C GLU* 4.8 7.0 - - - +
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Residues in contact with THR 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 3.8 30.4 + - + +
36C VAL* 4.1 21.3 + - + +
148C ALA* 3.4 5.0 - - - +
149C ILE* 2.7 54.3 + - + +
243C ASP* 5.4 0.2 - - - -
244C ASP* 1.3 76.8 - - - +
246C GLU* 1.3 86.9 + - - +
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B MET* 3.8 27.9 - - - +
36C VAL* 4.1 8.1 - - - +
37C PRO 4.5 2.4 - - - +
38C GLN* 4.7 4.5 - - - +
146C LYS* 3.6 28.9 + - + +
147C TYR 3.3 7.2 - - - +
148C ALA* 4.7 3.3 - - - +
149C ILE* 4.9 0.2 - - - -
244C ASP* 4.8 5.7 - - - +
245C THR* 1.3 106.4 + - - +
247C ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 4.2 5.8 - - + -
37C PRO 3.6 17.7 - - - +
38C GLN 3.9 5.2 - - - +
40C VAL* 3.8 28.0 - - + -
46C PHE* 3.7 36.3 - - + -
79C PRO* 4.0 18.8 - - + -
82C PHE* 4.5 9.4 - - + -
145C GLY 3.8 0.9 - - - +
146C LYS* 3.4 1.9 - - - -
147C TYR* 2.8 39.0 + - + +
149C ILE* 3.6 22.9 - - + -
246C GLU* 1.3 74.8 - - - +
248C VAL* 1.3 68.3 + - - +
249C LEU 3.9 0.4 + - - +
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Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU 4.3 0.2 - - - +
58B ASP* 4.9 0.7 - - - +
59B PRO* 4.1 25.1 - - + -
38C GLN* 3.0 29.6 + - - +
39C SER* 3.2 17.0 - - - +
40C VAL* 2.8 29.1 + - - +
145C GLY* 3.5 8.5 - - - +
146C LYS* 4.0 23.6 - - + -
247C ILE* 1.3 78.4 - - - +
249C LEU* 1.3 68.8 + - - +
250C GLN* 3.1 24.5 + - + +
254C ARG* 6.2 0.4 - - - +
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.5 27.1 - - + +
42C PRO* 4.0 19.7 - - + -
82C PHE* 4.3 14.4 - - + -
133C SER* 4.0 11.9 - - - -
134C PRO* 4.1 10.5 - - + +
136C PRO* 3.7 23.1 - - + -
142C ILE* 4.8 2.5 - - + -
143C HIS 4.0 3.8 - - - +
144C PHE* 3.4 47.1 - - + +
145C GLY* 2.8 36.3 + - - +
147C TYR* 4.2 15.6 - - + -
247C ILE* 3.9 2.8 + - - +
248C VAL* 1.3 70.7 - - - +
250C GLN* 1.3 57.9 + - - +
254C ARG* 5.1 0.3 + - - -
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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