Contacts of the strand formed by residues 93 - 98 (chain F) in PDB entry 5MG3
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 ASP 93 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C TRP* 4.1 1.4 - - - -
261D PRO* 4.9 0.3 - - - +
60F ILE 3.4 6.5 - - - +
61F THR* 2.6 29.3 + - - -
89F GLY* 3.2 3.6 - - - -
90F SER 2.9 32.0 + - - +
91F SER 3.7 0.4 - - - -
92F HIS* 1.3 104.5 + - - +
94F ILE* 1.4 65.5 + - - +
95F MET* 3.3 25.2 - - + +
129F LYS* 2.9 25.5 + - + -
268F PRO* 3.4 9.9 - - - +
269F VAL* 3.8 4.9 - - - +
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Residues in contact with ILE 94 (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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346C TRP* 3.5 51.1 - - + +
350C PHE* 5.9 1.8 - - + -
58F ILE 4.0 0.7 - - - +
59F GLU* 3.6 2.3 - - - -
60F ILE* 2.9 61.9 + - + +
61F THR* 4.8 0.2 - - - +
62F LEU* 3.8 25.8 - - + -
68F ILE* 4.0 14.6 - - + -
71F MET* 5.3 4.3 - - + -
88F PHE 3.6 7.6 - - - +
92F HIS 4.3 0.2 + - - -
93F ASP* 1.4 76.6 - - - +
95F MET* 1.3 60.2 + - - +
96F VAL* 4.3 15.7 - - + +
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Residues in contact with MET 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F VAL* 5.7 0.4 - - + -
58F ILE 3.5 5.2 - - - -
59F GLU* 4.1 27.6 - - + +
60F ILE 5.0 0.2 - - - +
88F PHE* 2.8 63.3 + - + +
89F GLY 4.4 0.2 - - - +
90F SER 4.5 4.5 - - - +
93F ASP* 3.3 34.1 - - + +
94F ILE* 1.3 80.4 - - - +
96F VAL* 1.3 61.2 + - - +
97F ARG* 3.1 14.3 - - - -
129F LYS* 5.2 0.4 - - - -
268F PRO* 4.2 16.6 - - + +
269F VAL* 4.0 29.2 - - + +
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C PHE* 4.4 11.7 - - + -
57F VAL* 3.5 3.8 - - - +
58F ILE* 2.7 53.5 + - + +
75F LEU* 4.7 4.5 - - + -
85F LEU* 3.6 39.3 - - + -
86F GLN 3.6 8.3 - - - +
87F ASN* 4.3 17.5 - - - +
88F PHE 5.1 0.9 - - - +
94F ILE* 4.8 15.9 - - + -
95F MET* 1.3 82.1 - - - +
97F ARG* 1.4 64.6 - - - +
98F MET* 3.7 5.6 - - - +
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Residues in contact with ARG 97 (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 TRP* 3.6 23.1 - - + +
56F THR 3.4 6.5 - - - +
57F VAL* 3.9 22.0 - - + -
86F GLN* 2.9 72.3 + - - +
87F ASN 3.7 3.6 + - - -
88F PHE* 3.6 24.0 - - - +
95F MET* 3.1 32.5 - - - -
96F VAL* 1.4 78.6 - - - +
98F MET* 1.4 61.8 + - - +
191F PHE 5.1 1.2 + - - -
192F HIS* 2.7 29.7 + - - +
193F ILE* 4.0 5.1 - - - +
194F GLU* 2.6 43.1 + - - +
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Residues in contact with MET 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F TRP* 4.1 6.7 - - - -
55F GLY* 3.9 3.2 - - - -
56F THR* 2.9 43.0 + - + +
58F ILE* 4.1 24.7 - - + +
75F LEU* 4.3 2.2 - - + -
80F PHE* 3.7 50.9 - - + -
84F MET* 3.5 20.2 - - + +
85F LEU* 3.6 22.7 - - + -
96F VAL* 3.7 11.4 - - - +
97F ARG* 1.4 83.2 - - - +
99F PRO* 1.4 78.1 - - + +
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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