Contacts of the helix formed by residues 93 - 102 (chain E) in PDB entry 3K75
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 93 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E SER* 1.3 57.0 + - - +
95E SER* 2.7 11.0 + - - +
96E SER* 2.4 38.5 + - - +
97E ILE* 2.7 28.5 + - + +
112E ARG* 5.7 1.8 - - + -
115E VAL* 3.4 34.1 - - + +
120E LYS* 5.8 5.3 - - - +
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Residues in contact with SER 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E THR* 1.3 77.6 + - - +
95E SER* 1.3 59.6 + - - +
97E ILE* 3.4 14.2 + - - +
98E ASN* 3.0 34.0 + - - +
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Residues in contact with SER 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E THR* 2.7 11.5 + - - +
94E SER* 1.3 78.4 + - - +
96E SER* 1.3 62.2 + - - -
97E ILE 3.1 1.3 - - - -
98E ASN* 3.4 24.7 + - - +
99E PHE* 3.7 6.9 + - - +
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Residues in contact with SER 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E THR* 2.4 29.7 + - - -
95E SER* 1.3 72.2 + - - +
97E ILE* 1.3 61.1 + - - -
99E PHE* 3.5 19.0 + - - +
100E LEU* 3.7 13.7 + - - +
115E VAL* 4.6 7.5 - - - +
120E LYS* 3.6 44.1 + - - +
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Residues in contact with ILE 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E THR* 2.7 26.0 + - + +
94E SER* 3.4 17.3 - - - +
95E SER 3.1 0.2 - - - -
96E SER* 1.3 75.3 - - - +
98E ASN* 1.3 64.1 + - - +
99E PHE 3.0 5.5 + - - -
100E LEU* 3.5 1.3 + - - +
101E THR* 2.9 30.6 + - - +
108E PRO* 4.7 9.2 - - + +
111E ALA* 3.7 16.6 - - + +
112E ARG* 3.4 41.5 - - + +
115E VAL* 3.3 28.3 - - + -
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Residues in contact with ASN 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E SER* 3.0 19.6 + - - +
95E SER* 3.4 15.0 + - - +
97E ILE* 1.3 81.4 - - - +
99E PHE* 1.3 57.6 + - - +
101E THR* 4.0 8.7 - - - -
102E ARG* 3.2 31.5 + - - +
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Residues in contact with PHE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E SER 3.7 5.5 + - - +
96E SER* 3.5 16.1 + - - +
97E ILE 3.0 0.6 - - - -
98E ASN* 1.3 79.2 - - - +
100E LEU* 1.3 70.6 + - + +
102E ARG* 3.6 37.2 + - - +
103E VAL* 4.2 7.7 + - + +
120E LYS 3.5 16.2 - - - -
121E THR* 3.6 7.4 - - - -
122E LEU* 3.1 52.3 - - + -
125E LEU* 5.6 0.2 - - + -
143E PHE* 4.9 5.1 - + - -
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E SER 3.7 8.7 + - - +
97E ILE 3.5 2.3 + - - +
99E PHE* 1.3 80.1 - - + +
101E THR* 1.3 60.6 + - - +
102E ARG 3.0 1.8 - - - -
103E VAL* 2.8 31.8 + - - +
106E ILE* 3.6 19.6 - - + +
111E ALA* 3.7 19.1 - - + +
114E LEU* 3.4 36.1 - - + -
115E VAL* 4.3 6.3 - - + -
119E ILE* 3.9 15.9 - - + +
120E LYS 3.9 17.5 - - - +
121E THR 4.5 2.2 - - - +
125E LEU* 3.3 33.9 - - + -
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Residues in contact with THR 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ILE* 2.9 25.2 + - - +
98E ASN* 4.0 9.7 + - - +
100E LEU* 1.3 78.9 - - - +
102E ARG* 1.3 58.8 + - + +
103E VAL 2.8 16.6 - - - +
106E ILE* 3.7 18.7 + - - +
107E GLY* 5.9 0.4 - - - -
108E PRO* 4.5 13.1 - - + +
111E ALA* 3.9 10.4 - - - +
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Residues in contact with ARG 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ASN* 3.2 22.1 + - - +
99E PHE* 3.6 29.3 - - - +
100E LEU 3.0 1.0 - - - -
101E THR* 1.3 77.2 - - + +
103E VAL* 1.3 58.8 + - - +
104E THR* 4.0 5.2 + - - +
143E PHE* 3.2 38.8 - - + -
147E GLU* 2.4 42.1 + - - +
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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