Contacts of the helix formed by residues 116 - 129 (chain A) in PDB entry 6BAA
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A TRP* 4.3 8.7 - - - +
100A LEU* 6.4 0.2 - - - -
114A ILE* 4.3 3.7 - - - +
115A HIS* 1.3 80.3 - - - +
117A PHE* 1.3 66.7 + - - +
118A SER* 3.5 17.3 + - - -
119A SER* 2.5 30.7 + - - -
120A ALA* 3.2 6.4 + - - +
140D GLU* 4.0 10.6 - - - +
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.9 26.0 - - + -
87A ALA* 4.3 7.0 - - + -
88A MET* 4.0 39.5 - - + -
91A TRP* 3.9 43.5 - + + +
116A SER* 1.3 75.1 - - - +
118A SER* 1.3 57.5 + - - +
120A ALA* 2.7 7.4 + - - +
121A PHE* 2.7 55.2 + + + -
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A SER* 3.5 12.0 + - - -
117A PHE* 1.3 83.8 - - - +
119A SER* 1.3 62.6 + - - +
121A PHE* 3.2 9.0 + - - +
122A LEU* 3.0 28.6 + - - +
140D GLU* 3.8 20.6 + - - -
146D ILE* 4.4 16.5 - - - +
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER 3.8 17.9 - - - -
114A ILE* 3.5 7.5 - - - +
115A HIS* 3.1 13.3 + - - -
116A SER* 2.5 34.6 + - - -
118A SER* 1.3 79.9 - - - +
120A ALA* 1.3 60.2 + - - +
122A LEU 3.5 0.3 + - - -
123A PHE* 3.2 17.0 + - - +
136A ARG* 3.3 19.1 + - - +
140D GLU* 3.3 29.7 - - - +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 4.1 7.6 - - - +
90A TRP* 4.6 5.4 - - + +
91A TRP* 3.8 39.3 - - + +
114A ILE* 4.0 16.6 - - + -
116A SER 3.2 5.8 + - - +
117A PHE* 2.7 12.6 + - + +
119A SER* 1.3 80.0 + - - +
121A PHE* 1.3 62.3 + - - -
123A PHE* 3.1 8.1 + - - +
124A SER* 3.1 20.6 + - - -
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 4.7 7.4 - - + -
83A TRP* 4.9 2.9 - - + -
84A LEU* 3.4 41.1 - - + -
87A ALA* 3.7 18.3 - - + +
117A PHE* 2.7 31.8 + + + +
118A SER* 3.2 13.2 + - - +
120A ALA* 1.3 73.6 - - - +
122A LEU* 1.3 67.5 + - + +
124A SER* 2.9 14.6 + - - -
125A ILE* 3.1 39.7 + - + -
146D ILE* 4.3 18.2 - - + -
150D ILE* 3.8 28.7 - - + -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER 3.0 18.6 + - - +
119A SER 3.8 4.9 - - - +
121A PHE* 1.3 79.7 - - + +
123A PHE* 1.3 61.1 + - - +
125A ILE* 3.3 5.9 + - + +
126A GLU* 3.1 33.3 + - + +
136A ARG* 3.3 31.9 - - - +
138D VAL* 3.4 18.6 - - + +
139D THR 3.7 18.2 - - - +
140D GLU* 4.5 2.2 - - + +
146D ILE* 4.0 33.2 - - + -
149D LEU* 3.7 30.3 - - + -
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TRP* 3.4 51.8 - + + -
111A VAL* 3.9 19.5 - - + -
114A ILE* 4.6 3.1 - - + -
119A SER 3.2 13.1 + - - +
120A ALA* 3.1 12.3 + - - +
121A PHE 3.1 0.6 - - - -
122A LEU* 1.3 78.2 - - - +
124A SER* 1.3 64.1 + - - +
126A GLU* 3.3 12.9 + - + +
127A VAL* 3.2 42.3 + - + +
136A ARG* 3.5 40.6 - - + +
138A VAL* 3.4 28.7 - - + -
149A LEU* 5.2 0.2 - - + -
133B PHE* 4.0 14.6 - + - -
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TRP* 2.6 33.6 + - - -
87A ALA* 3.6 20.6 + - - -
90A TRP* 4.5 4.3 - - - -
120A ALA 3.1 5.6 + - - -
121A PHE* 2.9 10.2 + - - -
123A PHE* 1.3 77.5 - - - +
125A ILE* 1.3 62.0 + - - +
127A VAL 3.2 8.8 + - - -
128A GLN* 3.3 14.6 + - - +
152A GLN* 2.9 32.9 + - - +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TRP* 3.4 52.7 + - + -
121A PHE* 3.1 37.8 + - + +
122A LEU* 3.5 12.1 - - + +
123A PHE 3.2 0.2 - - - -
124A SER* 1.3 77.7 - - - +
126A GLU* 1.3 62.9 + - + +
127A VAL 3.1 1.4 + - - -
128A GLN 3.5 0.2 + - - -
129A VAL* 3.2 25.9 + - + +
131A ILE* 4.7 3.8 - - + +
149D LEU* 4.4 14.6 - - + -
150D ILE* 4.7 8.1 - - + -
153D ASN* 3.4 28.7 - - - +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.1 20.6 + - + +
123A PHE* 3.3 11.4 + - + +
125A ILE* 1.3 77.5 - - + +
127A VAL* 1.3 59.2 + - + +
130A THR* 3.5 2.3 - - - -
131A ILE* 2.8 38.9 + - + -
132A GLY* 3.2 15.3 + - - +
133A PHE* 2.9 57.3 + - + +
134A GLY 4.0 3.3 + - - -
136A ARG* 2.9 39.8 + - - +
131B ILE* 4.7 2.8 - - - +
133B PHE* 5.2 4.1 - - + -
149D LEU* 6.0 1.8 - - + -
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 3.2 46.2 + - + +
124A SER 3.6 6.5 - - - +
125A ILE 3.1 1.0 - - - -
126A GLU* 1.3 77.7 - - - +
128A GLN* 1.3 66.2 + - - +
130A THR* 3.4 14.9 + - - +
149A LEU* 3.6 19.7 - - + -
152A GLN* 3.5 27.1 - - + +
153A ASN* 3.1 31.2 - - - +
131B ILE* 4.4 7.6 - - + +
133B PHE* 4.4 8.1 - - + -
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Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 5.9 2.0 - - - -
82A SER* 3.0 48.1 + - - +
83A TRP* 3.2 27.7 + - + +
86A PHE* 3.5 7.8 - - - -
124A SER 3.3 2.8 + - - -
127A VAL* 1.3 79.9 - - - +
129A VAL* 1.3 59.8 + - - +
130A THR* 3.1 8.4 + - - +
152A GLN* 3.3 42.2 + - + +
153A ASN* 5.1 2.9 - - - +
155A VAL* 5.9 0.2 - - - -
156A GLY* 3.6 28.0 - - - -
159A ILE* 4.6 1.2 - - - +
160A ASN* 4.3 15.2 + - - -
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TRP* 3.2 39.3 - - + +
125A ILE 3.2 12.3 + - - +
126A GLU 4.5 0.2 - - - -
128A GLN* 1.3 74.4 - - - +
130A THR* 1.3 68.8 + - - +
131A ILE* 3.3 12.5 + - + -
160A ASN* 5.7 2.2 - - - +
130D THR* 2.8 33.1 - - + +
153D ASN* 4.5 22.9 - - + +
157D LEU* 4.8 15.0 - - + -
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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