Contacts of the helix formed by residues 118 - 135 (chain A) in PDB entry 3B3T
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 ASN 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ARG* 3.7 7.9 - - - +
96A GLY* 3.8 2.6 - - - -
97A HIS* 3.2 48.5 + - + +
99A ASP 4.2 1.4 + - - -
114A GLY 3.3 1.2 + - - -
116A ASP 3.2 2.0 - - - +
117A ASP* 1.3 69.7 + - - +
119A ALA* 1.3 66.0 + - - +
120A SER 3.1 0.9 - - - -
121A GLY* 2.9 18.2 + - - -
122A ILE* 3.2 16.0 + - - +
178A LEU 3.0 20.8 + - - -
179A ASP* 3.2 22.5 + - - +
180A MET 2.9 22.5 + - - -
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Residues in contact with ALA 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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26A ILE* 4.1 13.7 - - + +
29A LEU* 3.8 36.7 - - + +
35A ARG* 3.3 8.3 - - - +
113A PRO 5.0 0.2 - - - +
114A GLY 2.9 19.2 + - - +
115A ALA* 3.3 12.5 + - - +
118A ASN* 1.3 77.3 - - - +
120A SER* 1.3 56.4 + - - +
122A ILE* 3.3 2.1 + - - +
123A ALA* 2.8 32.1 + - - +
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Residues in contact with SER 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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26A ILE* 3.9 13.9 - - - -
115A ALA 2.9 13.1 + - - -
116A ASP* 2.7 23.7 + - - -
119A ALA* 1.3 76.6 - - - +
121A GLY* 1.3 56.8 + - - +
123A ALA* 3.4 2.3 + - - +
124A ALA* 3.0 23.4 + - - +
180A MET* 3.5 0.5 - - - -
181A THR* 2.9 38.5 + - - -
182A ASN* 3.7 21.3 - - - -
272A ALA* 4.8 2.6 - - - +
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Residues in contact with GLY 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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96A GLY* 5.5 0.2 - - - -
118A ASN* 2.9 23.3 + - - -
120A SER* 1.3 75.7 + - - +
122A ILE* 1.3 66.0 + - - +
124A ALA* 3.3 2.7 + - - +
125A VAL* 3.0 29.6 + - - +
178A LEU* 3.6 18.8 - - - +
181A THR* 4.1 13.0 - - - -
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Residues in contact with ILE 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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25A THR* 5.0 1.1 - - + -
29A LEU* 3.8 21.8 - - + -
35A ARG* 6.0 0.4 - - - +
48A TRP* 5.9 0.2 - - + -
49A ILE* 3.9 25.6 - - + -
53A TRP* 4.8 4.2 - - + -
96A GLY* 3.4 29.8 - - - +
97A HIS 3.5 15.0 - - - +
98A LEU* 3.9 9.9 - - + -
118A ASN* 3.2 15.3 + - - +
119A ALA* 3.7 6.1 - - - +
121A GLY* 1.3 74.2 - - - +
123A ALA* 1.3 55.0 + - - +
125A VAL* 3.3 5.9 + - + +
126A THR* 2.8 46.4 + - - +
146A MET 4.9 0.4 - - - +
147A ALA* 3.7 20.9 - - + -
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Residues in contact with ALA 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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22A ILE* 3.5 34.5 - - + +
25A THR* 3.7 21.1 + - + +
26A ILE* 3.6 12.3 - - + -
119A ALA 2.8 22.1 + - - +
120A SER 3.7 3.8 - - - +
122A ILE* 1.3 74.2 - - - +
124A ALA* 1.3 56.3 + - - +
126A THR* 3.3 2.5 + - - -
127A GLU* 3.0 30.1 + - - +
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Residues in contact with ALA 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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22A ILE* 4.8 1.7 - - - +
120A SER 3.0 17.2 + - - +
121A GLY* 3.5 7.4 - - - +
123A ALA* 1.3 73.2 - - - +
125A VAL* 1.3 64.3 + - - +
127A GLU* 3.2 1.4 + - - -
128A VAL* 3.0 28.4 + - - +
178A LEU* 3.8 20.2 - - + -
181A THR* 4.6 7.4 - - + +
272A ALA* 4.7 2.5 - - + +
276A THR* 3.2 32.6 - - - +
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Residues in contact with VAL 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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53A TRP* 3.8 27.1 - - + -
94A ILE* 4.2 14.1 - - + +
95A GLY* 4.2 27.1 - - - +
96A GLY 4.6 1.1 - - - +
121A GLY 3.0 17.8 + - - +
122A ILE* 3.8 6.5 - - + +
124A ALA* 1.3 75.5 - - - +
126A THR* 1.3 64.0 + - - +
128A VAL* 3.2 9.3 + - - +
129A ILE* 3.0 22.2 + - + +
145A PHE* 4.0 24.5 - - + -
146A MET 4.8 1.8 - - - +
178A LEU* 4.2 14.8 - - + -
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Residues in contact with THR 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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25A THR* 4.3 18.8 - - + +
48A TRP* 6.1 0.3 - - - -
49A ILE* 5.3 0.2 - - - +
52A GLU* 4.3 13.0 - - + +
53A TRP* 2.9 29.0 + - + +
56A LEU* 3.6 21.3 - - + +
122A ILE* 2.8 30.1 + - - +
123A ALA* 3.5 9.3 - - - -
124A ALA 3.2 0.2 - - - -
125A VAL* 1.3 77.1 - - - +
127A GLU* 1.3 56.9 + - - +
129A ILE* 3.2 6.1 + - - +
130A ARG* 2.9 23.6 + - + +
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Residues in contact with GLU 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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17A VAL* 3.4 11.5 - - + -
18A ASP* 2.8 26.4 + - - +
21A GLN* 3.3 18.8 - - + +
22A ILE* 3.8 16.8 - - + +
123A ALA 3.0 16.4 + - - +
124A ALA 3.2 0.2 + - - -
126A THR* 1.3 73.2 - - - +
128A VAL* 1.3 65.6 + - - +
130A ARG* 2.8 43.0 + - - +
131A VAL* 3.0 25.3 + - + +
276A THR* 3.7 21.5 - - + -
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 6.2 0.2 - - - -
94A ILE* 4.5 10.8 - - + -
124A ALA 3.0 19.6 + - - +
125A VAL* 3.4 9.2 - - - +
127A GLU* 1.3 77.3 - - - +
129A ILE* 1.3 61.6 + - - +
131A VAL* 3.9 1.8 - - - +
132A LEU* 3.0 47.4 + - + +
145A PHE* 4.0 13.0 - - + -
178A LEU* 5.7 0.7 - - + -
276A THR* 3.5 28.5 - - + +
279A GLY* 4.1 7.0 - - - +
280A LEU* 3.8 29.3 - - + +
283A ALA* 4.4 6.7 - - + -
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Residues in contact with ILE 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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53A TRP* 3.5 44.2 - - + +
56A LEU* 3.9 20.0 - - + -
57A SER* 4.8 0.2 - - - -
80A MET* 3.6 26.9 - - + -
125A VAL 3.0 17.8 + - - +
126A THR 3.4 6.1 - - - +
128A VAL* 1.3 78.4 - - - +
130A ARG* 1.3 63.4 + - - +
132A LEU* 3.4 4.4 + - - +
133A SER* 2.8 39.8 + - - +
145A PHE* 3.5 39.3 - - + -
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Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLN* 3.0 22.4 + - - +
18A ASP* 3.9 7.9 + - - +
21A GLN* 3.7 31.4 - - - +
56A LEU* 3.8 30.7 - - + -
126A THR* 2.9 14.3 + - + +
127A GLU* 2.8 47.5 + - - +
129A ILE* 1.3 76.6 - - - +
131A VAL* 1.3 66.4 + - - +
133A SER* 3.7 2.7 - - - -
134A GLU* 2.8 81.2 + - + +
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Residues in contact with VAL 131 (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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13A TRP* 3.8 19.3 - - + +
16A GLN* 4.0 18.4 - - + +
17A VAL* 4.2 9.6 - - + +
127A GLU* 3.0 22.1 + - - +
128A VAL 4.0 2.0 - - - +
130A ARG* 1.3 99.4 - - - +
132A LEU* 1.3 64.8 + - - +
134A GLU* 3.4 3.3 + - - -
135A ASN* 2.8 44.6 + - - +
280A LEU* 3.8 25.6 - - + -
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Residues in contact with LEU 132 (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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13A TRP* 3.9 14.8 - - + -
60A LEU* 4.3 1.3 - - - +
82A ILE* 5.0 6.7 - - + -
128A VAL* 3.0 31.8 + - + +
129A ILE* 3.9 2.9 - - - +
131A VAL* 1.3 75.7 - - - +
133A SER* 1.3 61.5 + - - +
135A ASN* 3.3 3.4 + - - -
136A ASN 3.1 4.2 + - - -
137A PHE* 3.0 65.6 + - + +
143A ILE* 5.0 0.4 - - + -
145A PHE* 3.8 28.3 - - + -
280A LEU* 3.5 22.4 - - + -
283A ALA* 4.1 10.8 - - + -
284A ILE* 4.0 7.9 - - + -
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Residues in contact with SER 133 (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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56A LEU* 3.2 28.1 + - - -
57A SER* 3.8 4.2 - - - -
60A LEU* 3.7 30.0 - - - +
80A MET* 4.4 0.3 - - - +
129A ILE* 2.8 33.9 + - - +
130A ARG* 3.7 4.7 - - - -
132A LEU* 1.3 77.0 - - - +
134A GLU* 1.3 63.6 + - - +
136A ASN* 3.1 19.8 + - - +
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Residues in contact with GLU 134 (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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16A GLN* 5.2 5.2 - - - +
21A GLN* 5.5 0.3 + - - -
56A LEU* 5.7 0.6 - - + +
130A ARG* 2.8 61.4 + - + +
131A VAL* 4.0 4.5 - - - +
132A LEU 3.4 0.2 - - - -
133A SER* 1.3 76.4 - - - +
135A ASN* 1.3 64.9 + - - +
136A ASN* 3.4 11.1 + - - -
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Residues in contact with ASN 135 (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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13A TRP* 3.4 47.8 + - + -
16A GLN* 2.9 35.1 + - - +
131A VAL* 2.8 33.4 + - - +
132A LEU 4.1 0.9 - - - +
133A SER 3.1 0.8 - - - -
134A GLU* 1.3 80.5 - - - +
136A ASN* 1.3 71.8 + - - +
137A PHE 3.2 1.5 + - - -
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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