Contacts of the strand formed by residues 139 - 148 (chain C) in PDB entry 1BDF
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 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C LYS* 2.8 25.3 + - - +
104C LYS 2.9 15.3 - - - -
105C SER* 3.4 16.4 - - - -
133C LEU* 3.7 5.7 - - - +
137C ASN 4.0 3.9 + - - -
138C ALA* 1.3 77.7 - - - +
140C ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 140 (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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61C ILE* 4.2 13.9 - - + -
62C ASP 6.2 0.2 - - - -
71C LYS* 3.8 29.8 - - + +
74C VAL* 4.2 7.4 - - + -
81C ILE* 5.5 1.8 - - + -
102C LEU* 3.3 5.1 - - + +
103C ASN* 3.3 1.4 - - - -
104C LYS* 2.8 38.9 + - + +
110C VAL* 3.3 37.2 - - + -
131C CYS* 3.3 24.7 - - + -
133C LEU* 3.8 8.3 - - + -
139C SER* 1.3 76.5 - - - +
141C SER* 1.3 61.6 + - - +
142C MET* 3.8 19.1 - - + -
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Residues in contact with SER 141 (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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61C ILE* 4.6 0.8 - - - +
62C ASP* 2.9 55.2 + - - +
102C LEU 3.2 5.8 - - - -
103C ASN* 2.8 21.2 + - - -
140C ILE* 1.3 75.8 - - - +
142C MET* 1.3 59.1 + - - +
143C ARG* 3.7 8.6 + - - -
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Residues in contact with MET 142 (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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59C VAL* 3.9 19.3 - - + -
60C GLU 3.0 13.5 - - - +
61C ILE* 3.7 20.9 - - + -
81C ILE* 4.5 9.9 - - + -
85C LEU* 4.5 9.4 - - - -
100C LEU 3.6 1.0 - - - +
101C THR* 3.4 3.5 - - - -
102C LEU* 2.8 66.1 + - + +
103C ASN* 5.4 0.2 - - - +
130C ILE* 4.4 13.0 - - + -
131C CYS* 4.8 0.4 - - - -
140C ILE* 3.8 30.3 - - + -
141C SER* 1.3 76.0 + - - +
143C ARG* 1.3 64.0 - - - +
144C ILE* 4.0 13.2 - - + -
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Residues in contact with ARG 143 (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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59C VAL* 3.5 2.8 - - - -
60C GLU* 2.9 81.7 + - + +
61C ILE 4.1 0.2 - - - -
62C ASP* 2.7 49.4 + - - +
99C ILE* 3.9 19.5 - - + -
100C LEU 3.2 6.5 - - - +
101C THR* 4.3 14.1 - - + +
141C SER* 3.7 11.2 + - - -
142C MET* 1.3 74.4 - - - +
144C ILE* 1.3 61.9 + - - +
145C LYS* 3.8 1.6 + - - +
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Residues in contact with ILE 144 (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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56C VAL* 3.4 40.2 - - + -
58C GLU 3.7 2.9 - - - +
59C VAL* 4.2 4.7 - - + +
85C LEU* 3.7 23.3 - - + -
88C LEU* 4.7 3.1 - - + -
98C VAL 3.8 0.2 - - - +
99C ILE* 4.6 1.1 - - - -
100C LEU* 2.7 46.0 + - + +
102C LEU* 4.3 12.3 - - + -
115C ILE* 3.9 28.0 - - + -
130C ILE* 4.5 3.4 - - + -
142C MET* 4.0 25.8 - - + -
143C ARG* 1.3 72.3 - - - +
145C LYS* 1.3 61.1 + - - +
146C VAL* 3.6 7.1 + - + +
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Residues in contact with LYS 145 (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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56C VAL* 3.2 6.9 - - - +
57C THR* 2.9 38.6 + - - +
58C GLU* 2.6 55.8 + - + +
97C GLU* 3.7 29.2 + - + +
98C VAL 3.9 2.7 - - - -
99C ILE* 3.6 28.3 - - + -
143C ARG 3.8 3.1 + - - +
144C ILE* 1.3 69.5 - - - +
146C VAL* 1.3 61.2 + - - +
147C GLN* 4.0 14.4 - - + +
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Residues in contact with VAL 146 (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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54C CYS* 3.9 26.6 - - + -
55C ALA* 3.4 14.6 - - - +
56C VAL* 4.2 15.5 - - + +
88C LEU 6.2 0.2 - - - +
90C VAL* 4.3 18.4 - - + -
97C GLU* 3.2 4.7 - - - +
98C VAL* 2.9 47.2 + - + +
100C LEU* 3.7 36.3 - - + -
144C ILE* 4.0 2.7 - - + +
145C LYS* 1.3 76.7 - - - +
147C GLN* 1.3 62.1 + - - +
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Residues in contact with GLN 147 (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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54C CYS* 3.2 5.9 - - - -
55C ALA 2.7 40.5 + - - +
57C THR* 2.6 41.7 + - + +
58C GLU* 5.3 3.2 + - - -
96C ASP 3.5 13.9 - - - +
97C GLU* 3.4 26.5 - - + +
145C LYS* 4.0 8.6 - - + +
146C VAL* 1.3 78.2 - - - +
148C ARG* 1.3 62.8 + - - +
177C TYR* 3.4 13.1 + - + +
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Residues in contact with ARG 148 (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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52C PRO* 5.3 5.6 - - + -
53C GLY* 3.4 24.9 - - - +
54C CYS* 3.6 19.5 - - - +
92C VAL 3.3 23.6 + - - +
93C GLN 3.8 1.6 + - - -
94C GLY* 3.0 30.1 + - - -
95C LYS 2.6 23.1 + - - +
96C ASP* 3.2 42.6 + - + +
147C GLN* 1.3 75.1 - - - +
149C GLY* 1.3 63.8 + - - +
177C TYR* 3.9 2.6 + - - -
1D MET* 5.7 4.7 - - + -
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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