Contacts of the strand formed by residues 126 - 132 (chain C) in PDB entry 4I7Z
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 GLU 126 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C VAL* 4.1 13.3 - - + +
50C VAL 3.1 15.5 - - - +
51C LYS* 3.1 32.4 + - + -
52C ILE* 5.7 0.2 - - - -
123C GLN 4.6 2.4 + - - +
124C TYR* 3.7 17.7 - - - +
125C GLN* 1.3 80.9 - - + +
127C ILE* 1.3 62.3 + - - +
128C VAL* 4.2 12.5 + - + +
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Residues in contact with ILE 127 (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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49C VAL* 4.6 1.1 - - - -
50C VAL* 2.7 41.8 + - + -
52C ILE* 4.0 25.8 - - + -
72C VAL* 4.1 16.2 - - + -
74C ALA* 5.0 1.8 - - + -
101C VAL* 4.4 19.7 - - + -
116C VAL* 3.7 27.4 - - + -
119C LEU* 4.5 4.9 - - + -
124C TYR* 4.0 20.4 - - + +
126C GLU* 1.3 77.7 - - - +
128C VAL* 1.3 67.2 + - - +
129C PHE* 3.4 30.2 - - + -
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Residues in contact with VAL 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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47C LYS* 3.6 28.3 - - + -
48C ALA 3.9 2.7 - - - -
49C VAL* 4.6 14.4 - - + +
94C LEU* 3.9 10.3 - - + -
97C GLU* 3.8 31.8 + - + +
98C VAL* 3.7 31.3 + - + +
103C PHE* 3.4 17.5 - - - -
126C GLU* 4.2 14.5 + - + +
127C ILE* 1.3 77.0 - - - +
129C PHE* 1.3 65.2 + - - +
130C PRO* 3.6 2.9 - - - +
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Residues in contact with PHE 129 (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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46C PHE 3.5 1.6 - - - +
47C LYS* 3.7 1.7 - - - -
48C ALA* 2.8 54.6 + - + +
50C VAL* 3.3 28.7 - - + -
74C ALA* 5.4 4.5 - - + -
76C LEU* 3.6 31.0 - - + -
78C LEU* 5.8 1.3 - - + -
84C ILE* 4.4 9.2 - - + -
103C PHE* 3.3 24.9 - + - -
114C LEU* 4.5 15.0 - - + -
116C VAL* 3.8 25.1 - - + -
127C ILE* 3.4 27.8 - - + -
128C VAL* 1.3 76.5 - - - +
130C PRO* 1.3 65.8 - - + +
131C VAL* 3.4 6.8 + - + +
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Residues in contact with PRO 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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45C VAL* 4.9 0.9 - - + -
46C PHE 3.7 5.2 - - - +
84C ILE* 3.4 15.4 - - + +
85C ALA* 2.9 21.6 + - + -
90C ILE* 3.8 32.3 - - + -
94C LEU* 4.0 15.5 - - + -
98C VAL* 3.6 29.2 - - + -
103C PHE* 3.5 27.4 - - + -
129C PHE* 1.3 79.1 - - - +
131C VAL* 1.3 59.3 + - - +
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Residues in contact with VAL 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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45C VAL* 3.3 1.9 - - - +
46C PHE* 2.8 93.9 + - + +
48C ALA* 4.1 10.5 - - + -
78C LEU* 4.0 22.9 - - + -
82C PHE* 3.9 15.7 - - + -
83C LYS 3.4 14.8 - - - +
84C ILE* 5.2 1.6 - - + -
85C ALA* 4.2 3.4 - - - -
129C PHE* 3.8 11.7 - - + +
130C PRO* 1.3 73.7 - - - +
132C LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 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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43C ASP* 3.8 5.8 - - - +
44C THR 3.4 31.9 - - - +
45C VAL* 4.0 6.3 - - + +
81C GLY 4.3 1.4 - - - +
82C PHE* 3.7 3.6 - - - -
83C LYS* 2.8 52.9 + - + +
84C ILE 4.7 0.7 - - - +
85C ALA* 3.9 18.2 - - + +
86C PRO* 3.9 21.3 - - + -
89C ARG* 3.6 35.0 - - - +
131C VAL* 1.3 74.7 - - - +
133C SER* 1.3 67.5 + - - +
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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