Contacts of the helix formed by residues 97 - 104 (chain C) in PDB entry 3DPR
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 THR 97 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ASN* 3.4 5.2 - - - +
51C SER* 3.5 13.0 - - - +
52C LEU 2.8 37.0 - - - +
53C VAL* 3.6 6.5 - - + -
54C PRO* 3.6 16.8 - - + -
94C LEU* 2.4 42.4 + - - +
96C THR* 1.3 72.3 - - - +
98C LEU* 1.3 70.4 + - - +
99C ILE* 3.2 0.4 - - - +
100C GLY 2.8 9.5 + - - -
101C GLU* 2.6 21.8 + - - -
212C VAL* 3.6 17.1 - - + +
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG 5.3 0.9 - - - +
249A PRO* 4.5 1.3 - - + -
250A PRO* 4.2 15.5 - - + -
183B ASN* 3.2 38.4 + - + +
185B THR* 4.3 2.2 - - - +
186B ILE* 4.0 36.1 - - + +
46C ILE* 4.3 17.0 - - + +
47C CYS* 5.7 0.2 - - - -
49C VAL* 4.3 21.1 - - + +
51C SER* 3.4 30.2 + - - +
97C THR* 1.3 71.4 - - - +
99C ILE* 1.3 53.1 + - - +
101C GLU* 3.0 7.1 + - - +
102C ILE* 2.7 41.0 + - + +
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C CYS* 3.7 38.1 - - + +
49C VAL 5.5 0.6 + - - +
51C SER* 4.2 0.4 - - - +
89C VAL* 4.6 8.1 - - + +
94C LEU* 6.4 0.7 - - + -
97C THR* 2.9 4.2 + - - +
98C LEU* 1.3 75.2 - - - +
100C GLY* 1.3 66.7 + - - +
102C ILE* 2.9 6.1 + - - +
103C SER* 2.5 39.0 + - - +
113C LEU* 4.5 7.6 - - + -
212C VAL* 3.5 46.2 - - + +
213C SER 4.5 0.9 - - - -
214C GLY* 3.9 14.6 - - - +
218C PHE* 3.6 33.9 - - + -
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Residues in contact with GLY 100 (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 VAL 3.2 25.1 - - - -
90C ALA* 4.4 1.6 - - - +
94C LEU 4.1 1.6 - - - -
95C ALA 2.8 17.7 - - - -
97C THR* 2.8 9.6 + - - -
99C ILE* 1.3 80.3 - - - +
101C GLU* 1.3 52.8 + - - -
103C SER* 3.3 8.0 - - - -
104C SER* 2.3 32.1 + - - -
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Residues in contact with GLU 101 (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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109A ARG* 2.6 36.4 + - - +
250A PRO* 3.8 26.5 - - + +
251A ARG 4.8 1.4 - - - +
252A ALA* 5.3 1.6 - - - -
273A ALA* 5.6 2.4 - - - +
180B LEU* 4.1 11.3 - - - +
95C ALA 2.6 6.5 + - - +
96C THR* 3.0 35.9 + - - +
97C THR 2.6 8.8 + - - +
98C LEU 3.3 7.4 - - - +
100C GLY* 1.3 69.7 - - - -
102C ILE* 1.3 65.2 + - + +
104C SER* 3.0 23.6 + - - -
105C TYR* 3.7 11.3 - - - -
228C LEU* 3.3 30.1 - - - +
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Residues in contact with ILE 102 (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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65A MET* 5.1 0.4 - - + -
70A PHE* 6.4 0.7 - - + -
113A LEU* 5.1 19.7 - - + -
43C LEU* 4.7 23.3 - - + -
46C ILE* 3.9 38.4 - - + -
47C CYS* 3.9 18.4 - - + -
98C LEU* 2.7 21.8 + - - +
99C ILE* 2.9 6.5 + - - +
101C GLU* 1.3 71.6 - - + +
103C SER* 1.3 66.1 + - - +
105C TYR* 2.8 30.8 + - + +
106C PHE* 3.9 11.2 - - + -
220C LEU* 3.9 16.4 - - + -
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Residues in contact with SER 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 3.4 33.6 - - - +
90C ALA* 4.8 2.0 - - - -
99C ILE* 2.5 34.1 + - - +
100C GLY 3.3 6.4 + - - -
102C ILE* 1.3 74.0 - - - +
104C SER* 1.3 51.5 + - - +
105C TYR 2.6 12.5 + - - -
106C PHE 2.8 23.7 + - - +
178C THR* 3.1 11.5 - - - +
218C PHE* 4.3 1.0 - - - -
220C LEU* 3.3 24.4 - - - +
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Residues in contact with SER 104 (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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90C ALA* 4.2 10.7 - - - +
95C ALA 4.0 0.2 + - - -
100C GLY 2.3 30.1 + - - -
101C GLU* 3.0 14.4 + - - -
102C ILE 2.8 1.6 + - - -
103C SER* 1.3 73.2 - - - +
105C TYR* 1.3 54.7 + - - +
224C ARG* 2.6 35.2 + - - +
226C THR* 3.2 17.0 - - - -
227C ASN* 4.4 1.8 - - - -
228C LEU* 3.2 35.8 - - - +
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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