Contacts of the helix formed by residues 115 - 129 (chain A) in PDB entry 3BMW
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A TRP* 3.5 4.3 - - - -
109A THR* 3.8 8.3 - - - -
111A PRO* 5.7 0.2 - - - -
114A GLY* 1.3 75.6 - - - -
116A PHE* 1.3 64.2 + - - +
117A THR* 3.2 12.6 + - - -
118A ASP* 2.9 29.7 + - - -
119A PHE 2.9 18.2 + - - -
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Residues in contact with PHE 116 (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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107A LYS 3.3 27.4 - - - -
108A ARG* 4.0 17.0 - - + -
109A THR* 3.6 18.5 + - + +
115A SER* 1.3 73.8 - - - +
117A THR* 1.3 56.8 + - - +
119A PHE* 3.3 2.8 + - + -
120A GLN* 2.9 24.3 + - - +
218A VAL* 4.0 14.4 - - + -
219A TRP* 3.6 28.0 - + - -
222A MET* 3.3 44.3 - - + +
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Residues in contact with THR 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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115A SER* 3.1 10.7 + - - -
116A PHE* 1.3 76.2 - - - +
118A ASP* 1.3 60.0 + - - +
120A GLN* 3.3 20.5 + - - +
121A ASN* 2.9 44.5 + - - +
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Residues in contact with ASP 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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32A ASN* 5.2 4.9 + - - -
54A TRP* 4.0 12.7 - - + +
55A GLN* 4.8 15.2 - - - +
58A ILE* 4.1 4.9 - - + +
113A PHE 4.8 0.7 - - - +
114A GLY* 3.3 15.2 - - - -
115A SER* 2.9 36.0 + - - +
117A THR* 1.3 76.0 - - - +
119A PHE* 1.3 57.5 + - - +
121A ASN* 3.1 16.8 + - - +
122A LEU* 2.9 27.4 + - - +
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Residues in contact with PHE 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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54A TRP* 3.8 32.2 - + + -
76A ILE* 4.0 12.6 - - + -
79A PRO* 3.9 6.5 - - + -
115A SER 2.9 12.7 + - - +
116A PHE* 3.5 12.3 - - + +
117A THR 3.3 0.2 - - - -
118A ASP* 1.3 76.0 - - - +
120A GLN* 1.3 58.6 + - - +
122A LEU* 3.1 9.9 + - + +
123A ILE* 3.0 55.0 + - + +
133A VAL* 5.1 0.7 - - + -
135A ILE* 3.7 20.4 - - + -
219A TRP* 3.9 22.9 - + + -
222A MET* 3.8 26.5 - - + -
224A ILE* 3.7 28.7 - - + -
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Residues in contact with GLN 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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116A PHE 2.9 13.9 + - - +
117A THR* 3.4 24.1 + - - +
119A PHE* 1.3 76.7 - - - +
121A ASN* 1.3 60.6 + - - +
123A ILE* 3.4 6.6 + - - +
124A ASN* 2.9 52.3 + - - +
222A MET* 4.0 16.3 - - + +
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Residues in contact with ASN 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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55A GLN* 5.1 4.8 + - - -
58A ILE* 3.6 16.0 - - + +
117A THR* 2.9 31.9 + - - +
118A ASP* 3.1 21.9 + - - +
120A GLN* 1.3 81.3 - - - +
122A LEU* 1.3 56.0 + - - +
124A ASN* 4.0 4.8 + - - +
125A THR* 2.7 38.9 + - - +
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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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54A TRP* 3.9 32.1 - - + +
57A ILE* 3.7 35.2 - - + -
58A ILE* 3.6 18.8 - - + +
61A ILE* 4.0 13.5 - - + -
74A ILE* 4.1 11.7 - - + -
76A ILE* 3.9 20.2 - - + -
118A ASP 2.9 12.9 + - - +
119A PHE* 3.1 13.7 + - + +
121A ASN* 1.3 74.1 - - - +
123A ILE* 1.3 66.8 + - + +
125A THR 3.9 0.2 - - - -
126A ALA* 2.9 27.0 + - - +
133A VAL* 4.8 7.6 - - + -
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Residues in contact with ILE 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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119A PHE* 3.0 40.0 + - + +
120A GLN* 3.7 7.6 - - - +
122A LEU* 1.3 74.8 - - + +
124A ASN* 1.3 64.3 + - - +
126A ALA* 3.5 0.7 + - - +
127A HIS* 3.0 58.6 + - + +
133A VAL* 3.7 35.0 - - + -
222A MET 3.6 21.1 - - - +
223A GLY* 3.7 19.5 - - - +
224A ILE* 4.0 7.6 - - - -
225A ASP* 5.1 0.4 - - - +
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Residues in contact with ASN 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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120A GLN* 2.9 43.5 + - - +
121A ASN* 4.0 5.3 + - - +
123A ILE* 1.3 82.7 - - - +
125A THR* 1.3 60.6 + - - +
127A HIS* 3.5 8.8 + - - +
128A ALA* 3.0 29.5 + - - +
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Residues in contact with THR 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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58A ILE* 3.9 21.0 - - + +
61A ILE* 3.8 22.2 - - + +
62A ASN* 3.5 34.4 + - - +
121A ASN* 2.7 25.6 + - - +
122A LEU 4.0 2.7 - - - -
124A ASN* 1.3 73.0 - - - +
126A ALA* 1.3 68.7 + - - +
128A ALA* 3.3 8.7 + - - +
129A HIS* 2.9 27.0 + - + +
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Residues in contact with ALA 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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61A ILE* 4.0 17.8 - - + +
74A ILE* 5.2 0.4 - - + -
122A LEU* 2.9 19.0 + - + +
123A ILE 3.6 1.6 - - - +
125A THR* 1.3 76.2 - - - +
127A HIS* 1.3 57.1 + - - +
129A HIS* 2.9 15.4 + - - -
131A ILE* 2.9 49.2 + - + +
133A VAL* 3.4 22.0 - - + -
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Residues in contact with HIS 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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6A VAL* 4.1 16.4 - - + +
123A ILE* 3.0 43.5 + - + +
124A ASN* 3.9 10.0 + - - +
125A THR 3.3 0.2 - - - -
126A ALA* 1.3 77.2 - - + +
128A ALA* 1.3 58.7 + - - +
130A ASN* 3.0 11.4 + - - +
131A ILE 3.3 17.7 - - - +
133A VAL* 5.0 1.2 - - + +
223A GLY* 3.7 5.8 - - - -
225A ASP* 2.6 37.8 + - - -
705A GOL 2.8 28.0 + - - +
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Residues in contact with ALA 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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124A ASN 3.0 17.8 + - - +
125A THR* 3.6 8.7 - - - +
126A ALA 3.3 0.2 - - - -
127A HIS* 1.3 75.6 - - - +
129A HIS* 1.3 69.9 + - + +
130A ASN 3.5 0.4 - - - -
705A GOL 3.3 31.5 + - - -
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Residues in contact with HIS 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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61A ILE* 3.5 34.4 + - + +
62A ASN* 3.2 32.5 + - - -
67A THR* 4.1 23.4 - - + +
125A THR* 2.9 20.5 + - + -
126A ALA 2.9 7.6 + - - +
128A ALA* 1.3 88.5 - - + +
130A ASN* 1.3 71.7 + - - +
131A ILE* 3.2 11.0 + - + +
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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