Contacts of the helix formed by residues 108 - 120 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B TYR* 3.5 48.2 - - + -
60B LEU* 4.1 20.6 - - + -
74B LEU* 3.9 25.8 - - + -
103B TYR* 2.9 45.2 + - + +
104B VAL* 4.8 0.7 - - + +
107B ASP* 1.3 82.1 - - + +
109B SER* 1.3 58.5 + - - +
110B GLY 3.4 2.2 - - - -
111B LEU* 3.2 12.9 + - + +
112B ILE* 2.9 42.3 + - + +
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL 3.4 21.0 + - - -
105B GLN* 3.8 13.6 + - - -
106B GLY 2.7 22.5 + - - -
108B LEU* 1.3 77.3 - - - +
110B GLY* 1.3 69.6 + - - +
112B ILE* 3.3 5.1 + - - +
113B PHE* 3.0 42.2 + - - -
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLY 4.4 0.4 + - - -
107B ASP 5.1 1.2 + - - -
108B LEU 3.4 0.4 - - - -
109B SER* 1.3 81.9 + - - +
111B LEU* 1.3 61.6 + - - +
113B PHE* 3.3 10.3 + - - +
114B ASP* 3.0 23.2 + - - +
117B ARG* 5.4 1.0 + - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 3.3 46.7 - - + +
53B TYR* 3.9 11.7 - - + -
60B LEU* 3.9 22.2 - - + -
107B ASP 5.2 2.8 + - - +
108B LEU* 3.2 18.9 + - + +
110B GLY* 1.3 76.8 - - - +
112B ILE* 1.3 62.6 + - - +
114B ASP* 3.2 8.1 + - + +
115B GLU* 3.0 21.8 + - + +
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 4.2 10.8 - - + -
70B MET* 3.7 23.2 - - + +
72B LEU* 4.1 16.4 - - + -
104B VAL* 4.1 27.6 - - + +
108B LEU* 2.9 33.1 + - + +
109B SER* 3.3 4.7 + - - +
111B LEU* 1.3 75.6 - - - +
113B PHE* 1.3 60.4 + - + +
115B GLU* 3.3 8.4 + - - +
116B ALA* 2.9 26.9 + - - +
133B ILE* 4.2 15.5 - - + -
150B ILE* 4.2 26.5 - - + -
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B SER* 3.0 38.2 + - - +
110B GLY* 3.8 7.0 - - - +
112B ILE* 1.3 78.3 - - + +
114B ASP* 1.3 58.2 + - - +
116B ALA* 3.6 3.6 - - - +
117B ARG* 2.9 42.6 + - - +
126B ASN* 3.5 62.4 - - + +
129B LEU* 3.8 23.9 - - + +
130B ALA* 4.0 17.5 - - + -
133B ILE* 4.3 11.7 - - + -
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLY 3.0 14.1 + - - +
111B LEU* 3.7 12.4 - - + +
112B ILE 3.2 0.2 - - - -
113B PHE* 1.3 74.6 - - - +
115B GLU* 1.3 67.8 + - - +
117B ARG* 3.2 14.6 + - - +
118B ASN* 2.9 46.9 + - - +
122B GLN* 5.0 4.0 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 4.6 8.1 - - + +
62B ARG* 2.9 47.9 + - - -
70B MET* 3.5 24.8 - - + +
71B HIS 5.5 0.3 + - - -
72B LEU* 3.9 20.1 - - + +
111B LEU* 3.0 13.6 + - + +
112B ILE* 3.3 11.0 + - - +
114B ASP* 1.3 78.8 - - - +
116B ALA* 1.3 56.9 + - - +
118B ASN* 3.2 9.4 + - - +
119B CYS* 2.9 47.9 + - - -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B MET* 3.6 20.6 - - + -
112B ILE 2.9 16.1 + - - +
113B PHE* 3.6 6.3 - - - +
115B GLU* 1.3 77.1 - - - +
117B ARG* 1.3 57.1 + - - +
119B CYS* 3.1 4.0 + - - +
120B LEU* 2.8 36.4 + - - +
129B LEU* 3.8 25.8 - - + -
133B ILE* 4.5 8.3 - - + -
152B THR* 4.6 5.6 - - + -
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLY 5.4 0.8 + - - -
113B PHE* 2.9 31.4 + - - +
114B ASP* 3.2 13.6 + - - +
116B ALA* 1.3 75.6 - - - +
118B ASN* 1.3 63.8 + - - +
120B LEU* 3.6 0.4 - - - -
121B SER* 3.1 43.5 + - - +
122B GLN* 3.4 42.9 + - - +
124B LEU 2.9 28.0 + - - +
125B THR* 3.8 2.4 - - - +
126B ASN* 2.9 39.1 + - - +
129B LEU* 3.7 8.4 - - + +
704B SO4 4.8 1.0 + - - -
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Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASP* 2.9 42.2 + - - +
115B GLU* 3.6 10.3 - - - +
117B ARG* 1.3 78.6 - - - +
119B CYS* 1.3 64.1 + - - +
120B LEU 5.0 0.9 - - - +
122B GLN* 4.5 9.3 + - - -
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Residues in contact with CYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 3.4 49.1 + - - +
70B MET* 3.9 11.4 - - + -
115B GLU* 2.9 43.4 + - - +
116B ALA 3.8 0.2 - - - +
118B ASN* 1.3 80.8 - - - +
120B LEU* 1.3 75.0 + - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 3.6 21.7 + - + -
70B MET* 4.3 1.1 - - + +
116B ALA 2.8 18.5 + - - +
117B ARG 3.6 1.8 - - - -
118B ASN 4.9 1.1 - - - +
119B CYS* 1.3 91.3 - - + +
121B SER* 1.3 63.9 + - - +
124B LEU* 3.7 11.4 - - + -
129B LEU* 4.4 4.9 - - + -
132B TYR* 3.8 36.1 - - + -
152B THR* 3.8 24.5 - - + +
154B ASP* 4.4 0.4 - - - +
222B TYR* 3.5 28.9 + - + +
225B TRP* 4.0 13.7 - - + -
226B LEU* 5.5 0.9 - - - +
704B SO4 4.4 3.3 + - - -
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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