Contacts of the strand formed by residues 125 - 134 (chain S) in PDB entry 6O81
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 LYS 125 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89S TYR* 3.4 2.9 - - - -
90S LYS* 2.8 37.4 + - - +
91S LEU* 5.0 2.4 - - - +
124S PHE* 1.3 73.7 - - - +
126S LEU* 1.3 61.9 + - - +
127S VAL* 4.1 1.9 + - - +
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Residues in contact with LEU 126 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S VAL* 4.3 11.8 - - - +
38S ARG* 5.5 13.1 - - + +
87S LYS* 4.9 16.6 - - + -
88S ILE 4.7 2.7 - - - +
89S TYR* 4.1 17.7 - - + +
124S PHE 4.3 0.6 + - - -
125S LYS* 1.3 74.6 - - - +
127S VAL* 1.3 63.0 + - - +
128S ARG 5.4 1.6 - - - +
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Residues in contact with VAL 127 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S HIS 4.5 6.2 - - - +
34S GLU 4.1 6.8 - - - +
35S VAL* 3.8 27.1 + - + +
38S ARG* 5.4 6.5 - - - +
41S THR* 5.5 0.3 - - - -
88S ILE 4.4 5.4 + - - +
125S LYS 4.1 1.7 + - - +
126S LEU* 1.3 76.1 - - - +
128S ARG* 1.3 64.2 + - + +
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Residues in contact with ARG 128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33S HIS* 5.2 13.2 - - + +
38S ARG* 6.5 0.7 - - - +
41S THR* 4.3 14.4 - - - -
42S ILE* 6.4 1.3 - - + -
87S LYS* 4.7 0.8 - - - -
88S ILE* 3.6 26.1 + - - +
126S LEU* 5.7 1.6 - - - +
127S VAL* 1.3 82.1 + - + +
129S HIS* 1.3 61.2 + - - +
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Residues in contact with HIS 129 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S ARG* 5.0 11.1 - - - +
39S GLN 4.2 21.1 - - - +
40S ALA* 4.9 0.4 - - - -
41S THR* 3.4 15.4 + - - +
42S ILE* 3.2 27.1 + - - +
85S ASN* 5.8 1.8 - - + -
86S ALA 3.2 20.0 - - - +
87S LYS* 4.2 9.0 - - + +
128S ARG* 1.3 75.6 - - - +
130S VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 130 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S ILE* 3.5 7.4 - - + +
44S ILE* 4.9 13.2 - - + -
84S ALA 3.6 2.3 - - - +
85S ASN* 4.6 0.9 - - - -
86S ALA* 2.9 40.9 + - + +
88S ILE* 6.0 3.7 - - + +
129S HIS* 1.3 76.1 - - - +
131S SER* 1.3 61.9 + - - +
132S PHE* 3.7 1.9 + - + +
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Residues in contact with SER 131 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40S ALA* 5.6 2.7 - - - -
42S ILE 2.9 11.1 + - - -
43S ASN* 3.5 6.0 - - - +
44S ILE* 2.9 26.5 + - - +
83S TYR* 4.9 12.8 - - - -
84S ALA 3.5 8.1 - - - -
85S ASN* 4.4 6.7 - - - +
130S VAL* 1.3 70.7 - - - +
132S PHE* 1.3 62.9 + - - +
133S VAL* 3.5 2.1 + - - +
334S GLY 3.5 25.4 - - - -
335S GLY* 4.1 12.8 - - - -
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Residues in contact with PHE 132 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S ILE* 3.3 12.8 - - + +
46S THR* 5.6 7.0 - - - -
58S VAL* 5.0 13.0 - - + -
82S GLY 3.4 2.8 - - - +
83S TYR* 3.4 3.2 - - - -
84S ALA* 2.9 43.0 + - + +
86S ALA* 6.3 1.6 - - + -
130S VAL* 3.7 3.5 + - + +
131S SER* 1.3 70.6 - - - +
133S VAL* 1.3 60.5 + - - +
134S ASP* 3.7 2.6 + - + +
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Residues in contact with VAL 133 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S ASN* 6.0 1.8 - - + -
44S ILE 2.9 15.9 + - - +
45S GLY* 4.0 6.8 - - - -
46S THR* 3.3 26.6 + - - +
81S LEU* 5.3 6.3 - - + -
82S GLY 3.5 5.8 - - - +
83S TYR* 3.7 28.9 - - + -
131S SER 3.5 2.0 + - - +
132S PHE* 1.3 70.3 - - - +
134S ASP* 1.3 61.3 + - - +
135S CYS* 4.0 1.4 + - - +
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Residues in contact with ASP 134 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S THR* 4.6 9.9 - - - -
54S LYS* 5.1 20.0 - - + +
55S SER* 5.6 5.4 - - - +
58S VAL* 5.8 5.6 - - + -
80S LYS 4.8 0.2 - - - +
81S LEU* 4.3 1.3 - - - -
82S GLY* 2.9 35.8 + - - +
132S PHE* 3.7 3.9 + - + +
133S VAL* 1.3 71.4 - - - +
135S CYS* 1.3 61.4 + - - +
136S PRO 4.3 0.3 - - - -
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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