Contacts of the strand formed by residues 108 - 113 (chain C) in PDB entry 3DLX
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 ILE 108 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLY* 5.3 0.4 - - - -
85C LEU* 3.7 15.3 - - + +
87C ALA* 3.9 12.3 - - + -
99C LEU* 3.8 31.6 - - + -
102C LEU* 3.8 30.4 + - + +
103C LEU* 3.8 22.0 - - + +
106C LYS* 3.4 8.3 - - - +
107C GLN* 1.3 83.2 - - - +
109C LYS* 1.3 61.8 + - - +
110C ARG 3.5 28.0 - - - +
111C MET* 3.9 6.5 - - + -
125C GLN* 4.7 5.9 - - - +
130C GLU 5.0 3.6 - - - +
131C LEU* 3.8 19.3 - - + +
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Residues in contact with LYS 109 (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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84C GLY* 3.9 26.5 - - - +
85C LEU 2.9 10.7 + - - +
86C THR* 5.9 1.6 - - - +
108C ILE* 1.3 75.0 - - - +
110C ARG* 1.3 61.3 + - + +
130C GLU 4.8 4.3 - - - +
131C LEU* 3.6 6.8 - - - +
132C GLU* 3.0 52.7 + - - +
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Residues in contact with ARG 110 (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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85C LEU 3.3 3.0 + - - -
86C THR* 3.2 26.6 - - + +
87C ALA 2.7 32.2 + - - -
108C ILE* 3.5 7.3 - - - +
109C LYS* 1.3 83.4 - - + +
111C MET* 1.3 64.9 + - - +
112C VAL* 4.4 1.1 - - - -
132C GLU* 3.0 44.3 + - - +
133C VAL 4.5 0.7 - - - +
134C GLU* 3.0 37.0 + - - +
172C ILE* 3.9 20.8 - - - +
182C ILE* 4.8 10.5 - - - +
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Residues in contact with MET 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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87C ALA* 3.3 17.9 - - - +
89C SER* 4.3 2.7 - - - -
91C ASN 3.7 13.2 - - - +
92C ALA* 3.9 17.7 - - + -
99C LEU* 2.9 38.4 - - + -
103C LEU* 4.3 4.7 - - + -
108C ILE* 3.9 14.1 - - + -
110C ARG* 1.3 78.2 - - - +
112C VAL* 1.3 61.9 + - - +
113C SER* 3.1 29.2 - - - +
122C PHE* 4.3 5.2 - - + -
131C LEU* 4.1 19.7 - - + -
132C GLU 2.9 9.8 + - - +
133C VAL* 3.3 12.7 - - + +
134C GLU 2.9 24.8 + - - -
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C THR* 4.2 22.7 - - + -
87C ALA 2.8 8.9 + - - -
88C VAL* 3.6 19.2 - - + +
89C SER 3.0 25.6 + - - +
110C ARG* 4.4 1.8 - - - -
111C MET* 1.3 77.1 - - - +
113C SER* 1.3 58.1 + - - +
134C GLU* 3.6 33.0 - - + +
136C THR* 3.6 21.3 - - + +
141C LEU* 3.9 20.4 - - + +
144C ARG* 5.3 1.3 - - - +
203C ILE* 4.4 11.0 - - + -
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Residues in contact with SER 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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89C SER 2.8 21.0 + - - -
90C ASN 3.4 7.4 - - - -
91C ASN 4.6 0.2 - - - -
111C MET* 3.1 29.7 - - - +
112C VAL* 1.3 74.8 - - - +
114C SER* 1.3 60.7 + - - +
116C VAL* 3.5 23.6 - - - -
133C VAL* 4.9 1.8 - - - -
134C GLU 3.2 9.2 + - - +
135C LEU* 3.3 6.8 - - - +
136C THR* 2.9 24.1 + - - -
141C LEU* 4.2 5.4 - - - -
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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