Contacts of the strand formed by residues 127 - 132 (chain C) in PDB entry 2F8X
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 LEU 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.8 4.6 - - + +
38C HIS* 4.3 5.6 - - + -
53C PHE* 3.8 16.6 - - + -
57C PRO* 3.5 36.1 - - + -
89C ILE* 4.5 11.4 - - + -
90C GLY 3.2 5.6 - - - +
91C ILE* 3.3 29.2 - - + -
114C LEU* 4.3 8.1 - - + -
125C PHE* 4.0 4.5 - - + -
126C MET* 1.3 72.0 - - - +
128C SER* 1.3 61.1 + - - +
129C VAL* 5.3 3.1 - - + -
142C PHE 4.0 0.2 - - - +
143C LEU* 3.1 10.0 - - - +
144C SER* 2.5 49.8 + - - +
147C ILE* 3.9 14.8 - - + -
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Residues in contact with SER 128 (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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89C ILE* 3.2 4.3 - - - +
90C GLY* 2.6 43.7 + - - -
92C GLY* 4.2 20.6 - - - -
98C MET* 3.6 9.6 - - - +
126C MET 3.6 1.0 + - - -
127C LEU* 1.3 73.6 - - - +
129C VAL* 1.3 62.4 + - - +
130C LYS 3.9 0.8 + - - -
141C VAL* 3.6 19.6 - - - +
142C PHE 4.0 2.7 - - - -
143C LEU* 4.6 8.1 - - - +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 5.2 1.1 - - + -
36C ILE* 3.6 24.7 - - + -
59C VAL* 4.2 27.8 - - + -
87C ALA* 4.9 5.2 - - + -
88C PHE 3.1 6.1 - - - +
89C ILE* 3.5 28.7 - - + -
101C LEU* 5.2 1.1 - - + -
127C LEU* 5.2 2.2 - - + +
128C SER* 1.3 74.3 + - - +
130C LYS* 1.3 67.8 + - - +
131C MET* 3.9 14.1 + - + -
141C VAL* 3.6 3.1 - - - -
142C PHE* 2.8 42.9 + - + +
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Residues in contact with LYS 130 (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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87C ALA* 3.3 1.0 - - - -
88C PHE 2.8 27.8 + - - +
98C MET* 3.6 22.1 - - + +
128C SER 3.9 0.2 - - - -
129C VAL* 1.3 73.2 - - - +
131C MET* 1.3 72.4 + - - +
132C PHE* 4.4 8.0 - - + -
138C ASP* 3.3 22.4 + - - -
140C GLY 3.9 13.7 + - - -
141C VAL* 4.2 16.5 - - + +
52M GLU* 3.4 21.9 + - - +
55M HIS* 3.5 26.5 - - + +
56M THR* 3.2 36.8 + - - +
59M LEU* 3.9 18.6 - - + -
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Residues in contact with MET 131 (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* 3.7 28.3 - - + -
59C VAL* 5.2 1.6 - - - -
61C LEU* 3.6 18.2 - - + -
66C TRP* 2.9 44.4 - - + -
85C PRO* 5.0 1.3 - - + -
86C CYS 3.1 21.5 - - - +
87C ALA* 4.1 10.1 - - + +
103C LEU* 5.4 0.4 - - - -
129C VAL* 4.2 10.1 - - + +
130C LYS* 1.3 87.0 - - - +
132C PHE* 1.3 57.7 + - - +
138C ASP* 3.6 2.5 - - - +
139C ILE* 2.7 42.4 + - + +
140C GLY 3.0 19.4 + - - +
142C PHE* 4.4 4.3 - - + -
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Residues in contact with PHE 132 (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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85C PRO* 3.5 1.0 - - - +
86C CYS* 2.5 60.7 + - + +
88C PHE* 3.6 28.5 - + - -
130C LYS* 4.4 11.7 - - + -
131C MET* 1.3 77.2 - - - +
133C TYR* 1.3 75.2 + - - +
136C SER* 4.7 4.5 - - - -
137C ASP 3.1 15.9 - - - +
138C ASP* 4.0 8.1 - - - +
139C ILE* 3.9 10.0 - - - +
56M THR* 3.8 24.7 - - + -
59M LEU* 3.6 25.1 - - + -
60M HIS* 3.8 31.6 - + + -
63M CYS* 4.7 2.7 - - + -
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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