Contacts of the strand formed by residues 133 - 138 (chain C) in PDB entry 3SPD
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 ILE 133 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C MET* 4.1 22.0 - - + -
104C VAL* 6.3 0.9 - - + -
112C ILE* 4.2 13.7 - - + -
113C PHE* 4.3 15.3 - - + -
116C ALA* 4.6 5.8 - - + -
129C LEU* 3.3 27.8 + - + +
130C ALA* 3.7 13.5 + - - +
131C ASN 3.6 1.5 - - - -
132C TYR* 1.3 82.3 - - - +
134C LYS* 1.3 71.0 + - - +
135C VAL* 4.2 9.3 - - + +
150C ILE* 4.1 18.8 - - + -
151C MET 3.3 8.3 - - - +
152C THR* 4.1 6.7 - - + -
153C LEU* 4.0 4.2 - - - +
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Residues in contact with LYS 134 (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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133C ILE* 1.3 74.1 - - - +
135C VAL* 1.3 67.4 + - - +
136C GLY 4.4 0.2 - - - -
149C HIS 3.7 1.0 - - - +
150C ILE* 3.6 1.0 - - - -
151C MET* 2.9 60.0 + - + +
152C THR 4.2 2.9 - - - -
153C LEU* 3.7 25.9 + - + +
155C HIS* 2.7 36.1 + - - -
169C PHE 2.8 22.6 + - - +
170C THR* 3.9 5.3 - - - +
174C PHE* 3.9 20.9 - - + -
176C LYS* 4.4 21.1 - - - +
201C TRP* 5.9 1.6 - - - +
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Residues in contact with VAL 135 (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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101C VAL* 6.2 0.7 - - + -
104C VAL* 4.5 21.5 - - + -
133C ILE* 4.2 9.6 - - + +
134C LYS* 1.3 82.1 - - - +
136C GLY* 1.3 58.9 + - - +
148C LEU* 3.5 33.2 - - + -
149C HIS 3.2 5.2 - - - +
150C ILE* 4.2 22.4 - - + -
174C PHE* 3.8 2.9 - - - -
176C LYS* 3.3 9.2 - - - +
177C ILE* 2.9 40.1 + - + +
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Residues in contact with GLY 136 (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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135C VAL* 1.3 77.2 - - - +
137C PHE* 1.3 60.8 + - - -
148C LEU* 3.5 11.9 - - - -
149C HIS* 2.9 38.6 + - - +
174C PHE* 3.3 15.6 - - - -
175C VAL 3.1 13.5 - - - -
177C ILE* 3.9 2.5 - - - -
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Residues in contact with PHE 137 (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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74C LEU 5.5 0.2 - - - -
86C PRO* 3.6 28.5 - - + -
89C ILE* 4.5 11.0 - - + -
90C MET* 3.9 28.9 - - + -
100C LEU* 4.1 19.7 - - + -
136C GLY* 1.3 73.4 - - - -
138C HIS* 1.3 63.1 + - - +
146C LEU* 3.7 28.5 - - + -
147C HIS 3.4 15.0 - - - -
148C LEU* 3.7 31.0 - - + -
149C HIS* 4.4 3.1 - - - -
173C PHE 3.6 0.2 - - - +
174C PHE* 3.6 2.8 - - - -
175C VAL* 2.7 45.7 + - + +
177C ILE* 3.6 22.9 - - + -
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Residues in contact with HIS 138 (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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86C PRO* 3.5 22.4 - - - +
137C PHE* 1.3 75.1 - - - +
139C ALA* 1.3 63.9 + - - +
140C GLY 3.3 0.5 + - - -
141C PRO* 3.6 19.9 - - + +
147C HIS* 5.2 2.0 + - - +
149C HIS* 3.8 18.9 + + - +
168C SER* 3.3 46.0 + - - -
169C PHE* 3.3 36.2 - + - -
173C PHE* 3.5 17.7 - + + -
174C PHE* 4.2 6.5 - + - -
175C VAL* 4.7 0.4 - - - -
1G T 4.2 5.4 - - - -
2G A 3.6 23.7 + - - -
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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