Contacts of the strand formed by residues 228 - 234 (chain G) in PDB entry 3M4D
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 PHE 228 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55G ILE 3.7 0.7 - - - +
56G ARG* 3.2 6.3 - - - +
57G THR* 2.9 41.0 + - - +
85G LYS* 5.6 0.4 - - - -
86G VAL* 3.8 30.7 - - + -
102G TYR 3.5 3.1 - - - -
103G PRO* 3.7 15.9 - - + -
155G THR* 4.2 15.0 - - + -
167G TRP* 3.5 59.9 - + + -
169G VAL* 4.1 8.7 - - + -
224G PHE* 3.7 29.8 - + - -
226G PRO* 3.9 8.5 - - + -
227G ASP* 1.3 89.3 - - - +
229G ALA* 1.3 59.6 + - - +
230G THR* 5.3 0.2 - - - -
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Residues in contact with ALA 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 4.7 11.2 - - + -
54G VAL* 4.6 8.7 - - + -
55G ILE 3.5 4.9 - - - +
56G ARG* 4.4 27.4 - - - +
101G TYR* 3.1 5.4 - - - -
102G TYR* 2.8 46.2 + - + +
167G TRP* 3.4 5.9 - - - -
227G ASP 4.3 0.2 + - - -
228G PHE* 1.3 75.1 - - - +
230G THR* 1.3 62.9 + - - +
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Residues in contact with THR 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 6.2 0.9 - - - -
53G LEU 3.5 1.2 - - - +
54G VAL* 3.4 4.0 - - - +
55G ILE* 2.8 41.1 + - - +
57G THR* 5.7 0.3 + - - +
88G LEU* 3.6 28.0 - - + +
98G ILE* 4.3 13.2 - - + -
100G ASP 3.7 9.6 - - - +
101G TYR* 5.2 0.2 - - + -
165G VAL* 3.7 19.8 - - + +
167G TRP* 3.3 23.0 - - - -
228G PHE 5.3 0.3 - - - -
229G ALA* 1.3 72.6 - - - +
231G VAL* 1.3 65.3 + - - +
232G ILE* 4.2 14.5 + - + -
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Residues in contact with VAL 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LYS* 5.3 0.2 - - - +
5F ILE* 5.2 13.7 - - + +
7F ILE* 5.4 2.2 - - + -
52G LEU* 3.5 37.9 - - + -
53G LEU 3.3 9.2 - - - +
54G VAL* 4.5 10.5 - - + +
98G ILE* 3.7 3.1 - - - -
99G SER* 2.8 37.4 + - - +
100G ASP* 2.8 58.1 + - + +
230G THR* 1.3 74.6 - - - +
232G ILE* 1.3 59.5 + - - +
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Residues in contact with ILE 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LEU* 3.5 5.0 - - - +
53G LEU* 2.9 36.4 + - + +
55G ILE* 3.7 17.9 - - + -
90G LEU* 4.1 13.0 - - + -
96G ALA* 3.7 17.3 - - + -
97G GLN 3.1 13.2 - - - +
98G ILE* 4.6 7.0 - - + -
230G THR* 4.4 13.5 - - + +
231G VAL* 1.3 78.1 - - - +
233G THR* 1.3 64.2 + - - +
245G ILE* 3.5 33.0 - - + -
284G ILE* 4.5 7.2 - - + -
286G TRP* 3.6 28.3 - - + -
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Residues in contact with THR 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 4.0 15.9 - - + -
26A VAL* 4.6 4.2 - - - +
50G LYS* 3.6 22.9 - - + +
51G LYS 3.4 5.2 - - - +
52G LEU* 3.2 26.7 - - + -
96G ALA* 3.4 6.4 - - - +
97G GLN* 2.9 47.8 + - - +
99G SER* 3.3 28.3 - - - +
232G ILE* 1.3 75.3 - - - +
234G MET* 1.3 61.7 + - - +
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Residues in contact with MET 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G LYS* 3.6 5.3 - - - +
51G LYS* 2.9 37.9 + - + +
94G GLU* 5.7 0.4 - - - +
95G VAL* 3.5 28.0 - - + -
96G ALA* 3.8 12.1 - - + +
233G THR* 1.3 76.3 - - - +
235G ASP* 1.3 77.6 + - - +
236G ARG 3.4 0.2 + - - -
238G ALA* 4.3 1.3 - - - -
240G LYS 3.3 26.9 - - - +
241G GLN* 3.9 11.0 - - - +
242G GLN 4.9 0.7 - - - +
243G THR* 3.5 11.9 - - - +
286G TRP* 3.5 59.7 - - + +
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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