Contacts of the strand formed by residues 102 - 107 (chain C) in PDB entry 4JDA
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 102 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C PHE* 4.4 1.6 - - - -
87C ILE* 3.7 5.2 - - - +
88C ARG* 2.9 37.3 + - + -
89C VAL* 3.0 36.5 + - + +
100C GLY 3.5 10.3 - - - +
101C THR* 1.3 80.3 - - - +
103C ARG* 1.3 71.9 + - - +
117C VAL* 4.1 17.3 - - + -
118C GLU 3.5 4.9 - - - +
119C ILE* 3.7 18.2 - - + -
135C LEU* 4.1 17.5 - - + -
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Residues in contact with ARG 103 (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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72C PHE* 3.1 71.9 + - + +
73C ALA* 5.3 0.4 - - - -
75C PRO* 3.7 20.7 - - - +
79C LYS* 3.9 9.9 - - - +
85C CYS* 3.4 23.3 - - - -
86C THR 3.8 4.0 - - - -
87C ILE* 4.9 1.3 - - - +
88C ARG* 4.7 0.7 - - - -
102C ILE* 1.3 78.4 - - - +
104C GLU* 1.3 59.9 + - - +
105C VAL* 3.8 17.7 - - - +
117C VAL* 3.1 8.3 - - - +
118C GLU* 2.8 42.9 + - + +
132C PHE* 3.6 43.8 - - - -
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C SER 4.2 0.2 - - - +
85C CYS* 3.8 1.7 - - - -
86C THR* 2.9 32.6 + - - -
88C ARG* 3.0 49.3 + - + +
103C ARG* 1.3 73.4 - - - +
105C VAL* 1.3 64.4 + - - +
106C SER* 3.8 1.7 + - - -
115C THR* 3.5 26.9 + - - +
116C SER 3.4 6.1 - - - +
117C VAL* 4.1 15.5 - - + +
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PRO* 4.1 11.7 - - + -
82C ILE* 3.9 31.4 - - + -
84C SER 3.5 5.2 - - - +
85C CYS* 4.3 3.4 - - - +
103C ARG* 3.8 32.6 - - + +
104C GLU* 1.3 75.0 - - - +
106C SER* 1.3 59.2 + - - +
107C VAL* 4.1 2.2 - - + +
115C THR* 3.1 22.0 + - - -
116C SER* 2.9 27.4 + - - +
118C GLU* 6.4 0.4 - - + -
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ILE* 4.0 1.7 - - - -
83C LYS* 3.1 23.7 + - - +
84C SER* 2.7 37.1 + - - +
104C GLU 5.1 1.1 - - - -
105C VAL* 1.3 76.5 - - - +
107C VAL* 1.3 66.3 + - - +
114C SER 3.7 6.3 - - - -
115C THR* 4.5 3.1 - - - +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE 3.5 15.3 - - - +
82C ILE* 4.8 4.7 - - + +
83C LYS* 4.4 3.0 - - - +
105C VAL* 5.6 1.6 - - + -
106C SER* 1.3 77.2 + - - +
108C VAL* 1.3 82.5 + - - +
109C SER 3.9 0.2 + - - -
111C LEU* 4.0 13.0 - - + -
113C ALA* 3.3 23.1 - - + +
114C SER* 2.7 32.5 + - - +
115C THR* 3.6 10.5 - - - +
116C SER* 4.9 3.8 - - - +
139C HIS* 5.9 0.2 - - + -
301C A9S 3.6 34.3 - - + +
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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