Contacts of the strand formed by residues 228 - 234 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55F ILE 3.8 0.3 - - - +
56F ARG* 3.2 6.4 - - - +
57F THR* 2.9 40.4 + - - +
85F LYS 5.7 0.2 - - - -
86F VAL* 3.7 24.2 - - + -
102F TYR 3.6 2.9 - - - -
103F PRO* 3.8 11.7 - - + -
155F THR* 4.2 15.3 - - + -
167F TRP* 3.5 64.8 - + + -
169F VAL* 4.1 7.4 - - + -
224F PHE* 3.8 28.0 - + - -
226F PRO* 3.5 20.9 - - + -
227F ASP* 1.3 87.5 - - - +
229F ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 4.9 10.1 - - + -
54F VAL* 4.5 9.2 - - + -
55F ILE 3.5 3.4 - - - -
56F ARG* 4.1 23.8 - - + +
101F TYR* 3.1 5.4 - - - -
102F TYR* 2.9 44.8 + - + +
167F TRP* 3.5 5.1 - - - -
227F ASP 4.5 0.2 + - - -
228F PHE* 1.3 74.7 - - - +
230F THR* 1.3 63.4 + - - +
231F VAL* 5.5 0.4 - - - -
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Residues in contact with THR 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU 3.5 1.6 - - - +
54F VAL* 3.4 2.5 - - - -
55F ILE* 2.8 44.5 + - - +
57F THR* 5.7 0.3 + - - +
88F LEU* 3.6 29.9 - - + +
98F ILE* 4.4 8.5 - - + -
100F ASP 3.7 8.3 - - - +
101F TYR* 4.4 0.4 - - - +
165F VAL* 3.7 20.0 - - + +
167F TRP* 3.3 22.2 - - - -
228F PHE 5.4 0.2 - - - -
229F ALA* 1.3 71.7 - - - +
231F VAL* 1.3 66.6 + - - +
232F ILE* 4.0 19.4 + - + +
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Residues in contact with VAL 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 3.7 47.6 - - + +
7E ILE* 5.0 1.3 - - + -
52F LEU* 3.1 38.1 - - + -
53F LEU 3.4 3.8 - - - +
54F VAL* 4.2 9.9 - - + -
98F ILE* 3.6 4.3 - - - +
99F SER* 2.7 43.2 + - - +
100F ASP* 2.8 25.6 + - + +
101F TYR* 5.5 0.2 - - - -
229F ALA 5.5 0.2 - - - -
230F THR* 1.3 77.4 - - - +
232F ILE* 1.3 54.5 + - - +
37G LYS* 5.8 0.7 - - - +
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Residues in contact with ILE 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F LEU* 3.0 6.1 - - - +
53F LEU* 2.8 37.7 + - + +
55F ILE* 3.5 30.7 - - + -
90F LEU* 4.5 9.2 - - + -
96F ALA* 3.8 18.8 - - + -
97F GLN 3.2 13.9 - - - +
98F ILE* 4.5 7.6 - - + -
230F THR* 4.2 13.7 - - + +
231F VAL* 1.3 79.2 - - - +
233F THR* 1.3 71.7 + - - +
245F ILE* 3.6 21.1 - - + -
284F ILE* 4.5 8.3 - - + -
286F TRP* 3.6 16.6 - - + -
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Residues in contact with THR 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F HIS* 5.3 0.4 - - - +
50F LYS* 4.0 23.8 + - + +
51F LYS 3.4 6.1 - - - +
52F LEU* 3.2 27.4 - - + -
95F VAL 4.9 0.2 - - - +
96F ALA* 3.4 6.9 - - - +
97F GLN* 2.9 44.4 + - - +
99F SER* 3.5 24.4 - - - +
232F ILE* 1.3 73.1 - - - +
234F MET* 1.3 62.4 + - - +
24G ASP* 3.8 20.2 + - + +
26G VAL* 4.7 1.7 - - - +
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Residues in contact with MET 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 3.4 6.8 - - - +
51F LYS* 2.9 37.0 + - + +
95F VAL* 3.4 31.6 - - + -
96F ALA* 3.9 17.5 - - - +
233F THR* 1.3 76.5 - - - +
235F ASP* 1.3 73.4 + - - +
236F ARG 3.3 0.7 + - - -
238F ALA* 3.6 10.3 - - + -
240F LYS 3.2 27.6 - - - +
241F GLN* 4.2 9.0 - - - +
242F GLN 5.1 0.2 - - - +
243F THR* 4.3 5.2 - - - +
286F TRP* 3.6 52.9 - - + +
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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