Contacts of the strand formed by residues 121 - 127 (chain C) in PDB entry 6UWZ
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 SER 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B TYR* 2.4 42.7 + - - -
53C ASN* 3.4 7.6 + - - -
54C VAL 3.3 7.1 + - - -
55C PHE* 3.6 25.3 - - - -
102C ILE* 3.7 4.4 - - - +
103C THR 3.3 6.1 + - - -
104C LEU* 3.1 38.1 + - - +
120C PRO* 1.3 76.1 - - - +
122C ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 122 (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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102B TYR* 3.7 6.5 - - - -
52C THR 3.4 1.2 - - - +
53C ASN* 3.3 4.0 - - - +
54C VAL* 2.9 34.7 + - + +
56C LEU 6.3 0.2 - - - +
101C GLU 5.3 0.2 - - - +
102C ILE* 4.1 14.4 - - + -
103C THR* 3.7 8.3 - - - +
121C SER* 1.3 79.6 + - - +
123C ILE* 1.3 59.2 + - - +
124C TYR* 3.4 41.8 + - + -
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Residues in contact with ILE 123 (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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97B ASN* 3.5 18.2 - - - +
98B ASN* 3.2 17.3 - - - +
99B ASP 3.4 18.8 - - - +
100B GLY* 3.7 15.7 - - - +
102B TYR* 3.8 7.8 + - + +
41C LEU* 4.9 2.0 - - + -
51C THR* 4.0 13.9 - - + -
52C THR 3.2 6.7 - - - +
53C ASN* 3.3 39.5 - - + +
99C SER* 5.8 3.6 - - - -
103C THR* 3.6 11.2 + - - +
122C ALA* 1.3 70.7 - - - +
124C TYR* 1.3 63.0 + - - +
125C ARG* 3.7 30.0 + - - +
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Residues in contact with TYR 124 (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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50C MET 3.3 1.9 - - - +
51C THR* 3.3 4.0 - - - +
52C THR* 2.9 41.6 + - - +
54C VAL* 3.8 16.8 - - + -
56C LEU* 4.6 3.3 - - + +
90C ILE 4.6 0.9 + - - -
91C VAL* 4.3 2.9 - - - -
92C LEU* 3.5 36.0 + - + -
99C SER* 3.9 11.7 - - - -
100C PHE 3.0 27.9 + - - -
101C GLU* 3.7 11.5 - - - -
102C ILE* 3.5 23.0 + - + +
122C ALA* 3.4 27.9 - - + -
123C ILE* 1.3 76.1 - - - +
125C ARG* 1.3 61.9 + - - +
126C SER* 3.9 1.1 - - - -
144C MET* 4.3 6.3 - - + -
146C PHE* 3.7 29.0 - + - -
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Residues in contact with ARG 125 (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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98B ASN 4.5 5.9 + - - -
99B ASP* 4.8 7.7 - - - +
100B GLY 5.0 2.2 - - - +
49C GLU* 3.6 30.2 + - - +
50C MET 3.3 4.3 - - - -
51C THR* 3.6 25.9 + - + +
92C LEU* 4.3 1.8 - - - -
95C ASN* 3.3 10.3 - - - +
96C ASN 3.0 20.1 + - - -
97C ASP* 3.5 33.0 + - - +
99C SER* 5.8 0.8 + - - -
123C ILE* 3.7 39.9 + - - +
124C TYR* 1.3 74.0 - - - +
126C SER* 1.3 60.0 + - - +
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Residues in contact with SER 126 (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 GLU* 3.4 4.9 - - - -
50C MET* 2.7 65.7 + - - +
92C LEU* 4.0 15.0 - - - -
94C ASN* 3.2 23.6 - - - -
95C ASN* 4.1 0.9 - - - +
96C ASN* 4.3 2.9 - - - -
124C TYR 3.9 0.8 - - - -
125C ARG* 1.3 74.4 - - - +
127C SER* 1.3 60.9 + - - +
143C THR 3.7 6.8 + - - -
144C MET* 4.9 8.1 - - - -
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Residues in contact with SER 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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48C GLU* 3.6 12.3 - - - -
94C ASN* 2.8 42.0 + - - +
96C ASN* 4.1 11.3 - - - +
126C SER* 1.3 72.6 + - - +
128C CYS* 1.3 60.4 + - - +
143C THR* 4.6 1.9 + - - +
39D GLN* 3.6 27.7 + - - -
171D MET* 4.0 20.1 - - - +
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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