Contacts of the helix formed by residues 116 - 129 (chain B) in PDB entry 6C3P
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 SER 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B TRP* 4.2 8.5 - - - +
100B LEU* 4.4 0.2 - - - +
114B ILE* 4.9 1.6 - - - +
115B HIS* 1.3 80.5 + - - +
117B PHE* 1.3 57.5 + - - +
118B SER* 3.3 14.6 - - - -
119B SER* 2.7 45.3 + - - -
120B ALA* 3.2 5.9 + - - +
140C GLU* 3.5 8.5 - - - +
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Residues in contact with PHE 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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84B LEU* 4.3 22.0 - - + -
87B ALA* 3.7 19.5 - - + -
88B MET* 3.6 43.5 - - + -
91B TRP* 3.7 46.6 - + + +
116B SER* 1.3 72.8 - - - +
118B SER* 1.3 64.8 + - - +
120B ALA 3.2 1.9 + - - +
121B PHE* 2.9 25.6 + + + +
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Residues in contact with SER 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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116B SER* 3.0 12.4 + - - -
117B PHE* 1.3 80.7 - - - +
119B SER* 1.3 57.0 + - - +
121B PHE* 3.2 7.8 + - - +
122B LEU* 2.9 30.5 + - - +
140C GLU* 3.4 17.7 + - - +
146C ILE* 3.2 31.2 - - - +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER 4.6 1.9 + - - -
114B ILE* 3.5 29.6 - - - -
115B HIS* 3.4 12.2 + - - +
116B SER* 2.7 28.4 + - - -
118B SER* 1.3 71.9 - - - +
120B ALA* 1.3 55.4 + - - -
121B PHE 3.2 0.2 + - - -
122B LEU* 3.3 5.4 + - - +
123B PHE* 2.9 28.6 + - - +
136B ARG* 3.8 5.2 - - - +
140C GLU* 2.3 35.6 + - - -
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Residues in contact with ALA 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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87B ALA* 3.5 22.4 - - - +
90B TRP* 4.1 6.9 - - + -
91B TRP* 3.5 28.3 - - + +
114B ILE* 4.4 11.8 - - + +
116B SER 3.2 5.8 + - - +
117B PHE 3.2 5.4 + - - +
119B SER* 1.3 79.9 - - - +
121B PHE* 1.3 57.7 + - - +
123B PHE* 3.3 9.3 + - - +
124B SER* 2.9 32.4 + - - -
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Residues in contact with PHE 121 (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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80B LEU* 4.6 7.0 - - + -
83B TRP* 3.9 22.2 - + + -
84B LEU* 3.6 32.5 - - + -
87B ALA* 3.6 24.4 - - + +
117B PHE* 2.9 24.1 + + + +
118B SER* 3.6 8.7 - - - +
120B ALA* 1.3 74.4 - - - +
122B LEU* 1.3 66.4 + - - +
124B SER* 3.1 2.8 + - - -
125B ILE* 3.0 50.1 + - + +
146C ILE* 4.1 16.8 - - + -
150C ILE* 3.5 26.7 - - + -
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Residues in contact with LEU 122 (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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118B SER* 2.9 19.6 + - - +
119B SER 3.6 5.2 - - - +
121B PHE* 1.3 75.9 - - - +
123B PHE* 1.3 58.5 + - - +
125B ILE* 3.3 7.1 + - + +
126B GLU* 2.9 35.9 + - - +
136B ARG* 4.2 14.8 - - - +
138C VAL* 3.9 41.3 - - + +
139C THR 4.2 15.0 - - - +
140C GLU* 4.1 20.2 - - + +
146C ILE* 4.0 23.6 - - + -
149C LEU* 3.9 21.0 - - + +
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Residues in contact with PHE 123 (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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133A PHE* 3.7 17.0 - + - -
90B TRP* 3.3 53.2 - + + -
111B VAL* 3.6 20.6 - - + -
114B ILE* 4.9 3.1 - - + -
119B SER 2.9 17.4 + - - +
120B ALA* 3.5 7.6 - - - +
122B LEU* 1.3 77.9 - - - +
124B SER* 1.3 56.1 + - - +
126B GLU* 3.2 5.3 + - - +
127B VAL* 2.9 49.7 + - + +
136B ARG* 3.3 43.0 - - + +
137B MET* 4.3 0.2 - - - -
138B VAL* 3.4 27.4 - - + -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 3.6 23.8 - - - -
87B ALA* 3.0 28.6 + - - -
90B TRP* 3.1 14.4 - - - -
120B ALA 2.9 10.2 + - - -
121B PHE 3.1 5.1 + - - -
123B PHE* 1.3 76.9 - - - +
125B ILE* 1.3 58.1 + - - +
128B GLN* 2.9 28.6 + - - +
152B GLN* 3.3 24.8 + - - +
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Residues in contact with ILE 125 (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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83B TRP* 3.9 25.6 - - + -
121B PHE* 3.0 51.5 + - + +
122B LEU* 3.7 9.6 - - + +
124B SER* 1.3 76.1 - - - +
126B GLU* 1.3 64.2 + - + +
129B VAL* 3.0 41.3 + - + +
131B ILE* 5.0 2.7 - - + -
146C ILE* 5.2 0.4 - - + -
149C LEU* 4.2 18.6 - - + -
150C ILE* 3.8 18.6 - - + -
153C ASN* 3.3 27.8 - - - +
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Residues in contact with GLU 126 (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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131A ILE* 4.8 0.3 - - - +
133A PHE* 4.5 1.2 - - + -
122B LEU* 2.9 21.4 + - + +
123B PHE* 3.6 5.9 - - - +
125B ILE* 1.3 78.0 - - + +
127B VAL* 1.3 62.4 + - + +
130B THR 3.2 1.4 + - - -
131B ILE* 2.7 34.2 + - + -
132B GLY* 3.2 19.1 + - - +
133B PHE* 3.0 50.0 + - + +
134B GLY 4.5 0.7 + - - -
136B ARG* 2.7 55.0 + - - +
138C VAL* 5.9 0.5 - - - +
149C LEU* 5.9 3.4 - - + -
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Residues in contact with VAL 127 (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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131A ILE* 4.0 14.1 - - + +
133A PHE* 4.0 12.6 - - + -
123B PHE* 2.9 56.2 + - + +
124B SER* 3.7 3.1 - - - +
125B ILE 3.2 0.2 - - - -
126B GLU* 1.3 75.3 - - - +
128B GLN* 1.3 62.6 + - - +
130B THR* 2.8 24.9 + - - +
149B LEU* 3.6 25.1 - - + -
152B GLN* 4.0 20.9 - - + +
153B ASN* 3.6 15.5 - - - +
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Residues in contact with GLN 128 (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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79B PHE* 4.8 4.6 - - - -
82B SER* 2.7 37.5 + - - +
83B TRP* 2.9 30.6 - - - +
86B PHE* 5.2 0.4 - - - -
124B SER 2.9 9.2 + - - +
127B VAL* 1.3 81.0 - - - +
129B VAL* 1.3 60.7 + - - +
130B THR* 3.4 8.1 + - - +
152B GLN* 3.3 31.2 + - + +
153B ASN* 5.2 2.9 - - - +
156B GLY* 3.7 34.3 - - - +
159B ILE* 3.7 12.5 - - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 3.4 36.3 - - + +
125B ILE* 3.0 26.2 + - + +
128B GLN* 1.3 77.0 - - + +
130B THR* 1.3 75.9 + - - +
131B ILE* 3.7 14.8 - - + -
130C THR* 3.3 19.4 - - + +
153C ASN* 3.7 24.0 - - + +
157C LEU* 5.1 16.8 - - + -
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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