Contacts of the helix formed by residues 108 - 120 (chain C) in PDB entry 3SPD
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 LEU 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C TYR* 3.4 49.4 - - + -
60C LEU* 4.0 20.6 - - + -
74C LEU* 3.9 26.0 - - + -
103C TYR* 2.9 43.2 + - + +
104C VAL* 4.9 0.7 - - + +
107C ASP* 1.3 82.9 - - + +
109C SER* 1.3 59.3 + - - +
110C GLY 3.5 2.0 - - - -
111C LEU* 3.2 13.1 + - + +
112C ILE* 2.9 41.1 + - + +
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Residues in contact with SER 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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104C VAL 3.5 20.1 + - - -
105C GLN* 3.9 13.5 + - - -
106C GLY* 2.7 23.0 + - - -
108C LEU* 1.3 77.4 - - - +
110C GLY* 1.3 68.3 + - - +
112C ILE* 3.2 6.0 + - - +
113C PHE* 3.0 41.3 + - - -
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Residues in contact with GLY 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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106C GLY 4.4 0.4 + - - -
107C ASP 5.1 1.2 + - - -
108C LEU 3.5 0.2 - - - -
109C SER* 1.3 82.5 + - - +
111C LEU* 1.3 61.7 + - - +
113C PHE* 3.3 10.4 + - - +
114C ASP* 3.0 23.2 + - - +
117C ARG* 5.4 0.7 + - - -
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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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52C ILE* 3.3 46.4 - - + +
53C TYR* 3.9 18.2 - - + -
60C LEU* 4.0 16.6 - - + -
107C ASP 5.2 2.4 + - - +
108C LEU* 3.2 19.4 + - + +
109C SER 3.2 0.4 - - - -
110C GLY* 1.3 77.2 - - - +
112C ILE* 1.3 57.8 + - - +
114C ASP* 3.3 7.9 + - + +
115C GLU* 3.0 27.2 + - + +
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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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60C LEU* 4.1 10.1 - - + -
70C MET* 3.7 23.2 - - + +
72C LEU* 4.0 17.5 - - + -
104C VAL* 4.1 25.8 - - + +
108C LEU* 2.9 34.4 + - + +
109C SER* 3.7 4.5 - - - +
111C LEU* 1.3 76.8 - - - +
113C PHE* 1.3 59.6 + - + +
115C GLU* 3.3 8.3 + - - +
116C ALA* 2.9 27.0 + - - +
133C ILE* 4.2 13.7 - - + -
150C ILE* 4.2 30.3 - - + -
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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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109C SER* 3.0 37.3 + - - +
110C GLY* 3.7 7.6 - - - +
112C ILE* 1.3 77.7 - - + +
114C ASP* 1.3 57.4 + - - +
116C ALA* 3.4 4.1 + - - +
117C ARG* 2.9 42.2 + - - +
126C ASN* 3.5 61.2 - - + +
129C LEU* 3.8 18.7 - - + +
130C ALA* 3.9 24.0 - - + -
133C ILE* 4.3 12.3 - - + -
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Residues in contact with ASP 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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110C GLY 3.0 16.3 + - - +
111C LEU* 3.7 9.0 - - + +
113C PHE* 1.3 73.6 - - - +
115C GLU* 1.3 67.2 + - - +
117C ARG* 3.3 14.0 + - - +
118C ASN* 2.9 48.7 + - - +
122C GLN* 5.0 4.2 + - - +
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Residues in contact with GLU 115 (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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52C ILE* 4.4 7.7 - - + +
62C ARG* 2.9 49.0 + - - -
70C MET* 3.5 24.8 - - + +
71C HIS 5.5 0.5 + - - -
72C LEU* 3.8 20.9 - - + +
111C LEU* 3.0 15.5 + - + +
112C ILE* 3.5 10.3 - - - +
114C ASP* 1.3 77.0 + - - +
116C ALA* 1.3 56.3 + - - +
118C ASN* 3.3 9.1 + - - +
119C CYS* 2.9 48.0 + - - -
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Residues in contact with ALA 116 (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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70C MET* 3.6 22.6 - - + -
112C ILE 2.9 17.1 + - - +
113C PHE* 3.7 6.1 - - - +
115C GLU* 1.3 77.5 - - - +
117C ARG* 1.3 57.6 + - - +
119C CYS 3.1 0.4 + - - +
120C LEU* 2.8 36.6 + - - +
129C LEU* 3.8 26.5 - - + -
133C ILE* 4.6 6.1 - - + -
152C THR* 4.6 9.4 - - + -
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Residues in contact with ARG 117 (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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110C GLY 5.4 0.6 + - - -
113C PHE* 2.9 31.3 + - - +
114C ASP* 3.8 12.6 + - - +
116C ALA* 1.3 75.6 - - - +
118C ASN* 1.3 64.2 + - - +
120C LEU* 3.7 0.4 - - - -
121C SER* 3.2 42.9 + - - +
122C GLN* 3.4 43.4 + - - +
124C LEU 2.9 28.6 + - - +
125C THR* 3.8 2.6 - - - +
126C ASN* 2.9 37.8 + - - +
129C LEU* 3.8 8.6 - - + +
704C SO4 4.8 0.7 + - - -
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Residues in contact with ASN 118 (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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114C ASP* 2.9 41.7 + - - +
115C GLU* 3.7 9.1 - - - +
117C ARG* 1.3 78.6 - - - +
119C CYS* 1.3 63.8 + - - +
120C LEU 5.0 1.0 - - - +
122C GLN* 4.5 9.5 + - - -
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Residues in contact with CYS 119 (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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69C LYS* 3.4 44.8 + - - +
70C MET* 3.9 9.9 - - + -
115C GLU* 2.9 45.3 + - - +
116C ALA 3.1 0.2 + - - -
118C ASN* 1.3 80.7 - - - +
120C LEU* 1.3 75.8 + - + +
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Residues in contact with LEU 120 (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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69C LYS* 3.6 21.3 + - + +
70C MET* 4.2 0.9 - - + +
116C ALA 2.8 18.0 + - - +
117C ARG 3.7 1.8 - - - -
118C ASN 4.9 0.9 - - - +
119C CYS* 1.3 91.8 - - + +
121C SER* 1.3 64.8 + - - +
124C LEU* 3.7 12.8 - - + -
129C LEU* 4.3 5.6 - - + -
132C TYR* 3.8 34.8 - - + -
152C THR* 3.8 24.0 - - + +
154C ASP* 4.5 0.2 - - - +
222C TYR* 3.6 26.8 + - + +
225C TRP* 4.0 14.8 - - + -
226C LEU* 5.5 0.7 - - - +
704C SO4 4.4 2.6 + - - -
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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