Contacts of the strand formed by residues 164 - 170 (chain C) in PDB entry 3MX0
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 ASN 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C LEU 3.6 2.3 - - - +
99C LYS* 3.6 1.0 - - - -
100C PHE* 2.8 63.6 + - + -
101C THR* 4.2 1.6 - - - +
102C VAL 4.0 10.7 - - - +
147C PRO* 3.2 12.8 - - - +
148C ASP* 2.8 21.8 + - + +
149C GLU* 2.4 52.9 + - - +
162C LYS 4.3 2.0 + - - -
163C LEU* 1.3 69.8 - - - +
165C VAL* 1.3 59.4 + - - +
166C GLU* 4.4 4.0 - - + -
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Residues in contact with VAL 165 (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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97C GLU* 3.9 24.2 - - + +
98C LEU 3.6 2.9 - - - -
99C LYS* 4.1 28.3 - - + -
148C ASP* 3.7 14.2 + - - +
163C LEU* 3.1 11.8 + - + +
164C ASN* 1.3 72.0 - - - +
166C GLU* 1.3 73.9 + - - +
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Residues in contact with GLU 166 (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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96C ILE 3.6 0.5 - - - +
97C GLU* 3.4 5.3 - - - +
98C LEU* 2.7 54.5 + - + +
100C PHE* 3.7 26.0 - - + -
145C ILE* 4.2 9.8 - - + +
146C ALA 3.3 16.3 - - - +
148C ASP* 2.4 29.7 + - - +
164C ASN* 4.4 0.4 - - + -
165C VAL* 1.3 83.0 - - - +
167C GLU* 1.3 61.3 + - - +
168C ARG* 3.6 30.7 + - + +
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Residues in contact with GLU 167 (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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95C PHE* 4.1 20.8 - - - +
96C ILE 3.3 11.9 + - - +
97C GLU* 4.7 8.6 - - + +
98C LEU* 6.3 0.2 - - - -
166C GLU* 1.3 75.4 + - - +
168C ARG* 1.3 97.4 + - - +
169C SER* 4.4 4.6 + - - +
197C TYR* 2.8 28.9 + - - -
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Residues in contact with ARG 168 (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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95C PHE* 3.8 0.5 - - - -
96C ILE* 2.9 38.0 + - + +
98C LEU* 5.9 2.7 - - + -
121C LEU* 5.1 9.2 - - + -
142C ILE* 4.8 13.9 - - + -
143C ASP* 3.1 24.7 + - + +
144C THR 3.7 17.4 + - - -
145C ILE* 4.5 21.5 - - + +
146C ALA 4.8 4.6 + - - +
166C GLU* 3.6 26.1 + - + +
167C GLU* 1.3 92.5 + - - +
169C SER* 1.3 66.6 + - - +
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Residues in contact with SER 169 (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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93C ARG* 3.5 9.6 + - - -
94C ILE 3.1 6.7 - - - -
95C PHE* 3.2 39.2 - - - -
96C ILE* 5.2 3.6 - - - -
142C ILE* 4.6 9.9 - - - +
167C GLU* 4.4 7.6 + - - +
168C ARG* 1.3 80.4 - - - +
170C VAL* 1.3 72.0 + - - +
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Residues in contact with VAL 170 (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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93C ARG* 3.0 15.2 - - - +
94C ILE* 2.9 44.3 + - + +
96C ILE* 5.9 0.2 - - + -
123C TYR* 3.6 41.7 - - + +
142C ILE* 4.2 16.4 - - + -
169C SER* 1.3 82.8 - - - +
171C GLY* 1.3 64.4 + - - +
173C LEU* 3.9 6.4 - - + +
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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