Contacts of the strand formed by residues 109 - 114 (chain C) in PDB entry 1DS5
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 PRO 109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TRP* 3.7 25.8 - - + -
70C LEU* 3.7 28.3 + - + +
78C ILE* 3.9 29.2 - - + -
100C ILE* 5.2 0.7 - - + -
101C VAL 3.1 9.0 - - - +
102C ARG* 4.3 1.1 - - - -
107C LYS 3.0 8.6 - - - +
108C THR* 1.4 93.6 - - + +
110C SER* 1.3 70.4 + - - +
111C LEU* 6.4 0.2 - - + -
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Residues in contact with SER 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 4.3 5.8 - - - +
68C LYS 3.5 6.7 - - - -
69C ILE* 3.2 31.4 - - - +
70C LEU* 4.7 1.3 - - - +
100C ILE* 3.3 5.7 - - - +
101C VAL* 2.6 54.8 + - - +
108C THR 5.2 0.7 - - - -
109C PRO* 1.3 80.3 + - - +
111C LEU* 1.3 68.7 + - - +
112C ILE* 3.4 8.1 - - - +
194G PRO* 4.8 7.0 - - - +
195G MET* 4.8 4.0 - - - -
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Residues in contact with LEU 111 (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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66C ILE 3.6 2.1 - - - +
67C ILE* 3.6 0.9 - - - -
68C LYS* 2.9 34.4 + - + +
70C LEU* 3.7 29.4 - - + -
81C GLU* 3.3 42.2 - - + +
82C ILE* 4.0 19.3 - - + -
85C LEU* 4.5 4.0 - - + -
97C LEU* 4.2 8.1 - - + -
99C ASP 4.1 1.3 - - - -
100C ILE* 3.8 23.1 - - + -
109C PRO* 6.4 0.2 - - + -
110C SER* 1.3 81.4 - - - +
112C ILE* 1.3 59.9 + - - +
113C PHE* 3.6 22.9 + - + -
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Residues in contact with ILE 112 (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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39C TYR* 3.5 40.4 - - + +
65C CYS* 3.4 35.9 - - + -
66C ILE 3.1 4.7 - - - +
67C ILE* 3.9 15.3 - - + -
97C LEU* 4.0 1.1 - - - +
98C LEU* 2.9 33.2 + - + +
99C ASP* 3.0 15.4 + - + +
101C VAL* 3.5 22.0 - - + -
110C SER* 3.4 20.0 - - - +
111C LEU* 1.3 77.8 - - - +
113C PHE* 1.3 60.8 + - - +
195G MET* 4.5 1.1 - - + -
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Residues in contact with PHE 113 (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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65C CYS* 3.4 8.5 - - - +
66C ILE* 2.8 44.4 + - + +
68C LYS* 4.0 24.0 - - + -
81C GLU* 4.0 8.3 - - - -
85C LEU* 3.6 31.6 - - + -
95C VAL* 3.5 39.0 - - + -
96C LYS 3.4 13.5 - - - +
97C LEU* 3.8 9.2 - - + -
98C LEU* 3.5 5.1 - - - +
111C LEU* 3.6 27.8 - - + -
112C ILE* 1.3 72.9 - - - +
114C GLU* 1.3 66.8 - - - +
175C ASP* 5.8 5.2 - - - -
176C TRP* 6.2 0.4 - + - -
601C AMP 4.4 6.7 - - - +
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Residues in contact with GLU 114 (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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64C LYS 5.4 0.4 - - - -
65C CYS* 5.1 0.7 - - - +
66C ILE* 3.9 1.7 - - - +
95C VAL* 3.2 15.4 - - + -
96C LYS* 2.6 53.3 + - + +
98C LEU* 3.1 20.5 - - + +
113C PHE* 1.3 78.9 - - - +
115C TYR* 1.3 70.0 + - - +
116C VAL* 4.6 2.5 - - + -
170C LYS* 4.7 4.2 - - - -
172C ARG* 3.2 35.7 + - - -
601C AMP 3.2 17.0 + - - -
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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