Contacts of the helix formed by residues 118 - 130 (chain A) in PDB entry 2B9B
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 ALA 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A THR* 1.3 74.3 - - - +
119A ALA* 1.3 57.7 + - - +
121A VAL* 3.3 2.6 + - - +
122A THR* 2.9 33.2 + - - -
365C PHE* 3.7 17.9 - - + +
366C LEU* 3.7 20.0 + - - +
369C PHE* 3.4 54.1 + - + +
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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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117A THR* 3.1 8.8 + - - +
118A ALA* 1.3 77.5 - - - +
120A GLN* 1.3 61.5 + - + +
122A THR* 3.2 7.8 + - - -
123A ALA* 2.8 30.7 + - - +
366C LEU* 4.0 24.4 + - + +
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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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113A LEU* 4.8 0.4 - - - -
115A VAL 4.1 3.8 - - - +
116A ALA* 3.3 16.6 - - + +
117A THR* 3.0 39.2 + - - +
119A ALA* 1.3 77.3 - - + +
121A VAL* 1.3 58.5 + - - +
123A ALA* 3.2 5.5 + - - +
124A ALA* 2.9 25.3 + - - +
211A ILE* 4.3 21.4 - - - +
212A THR* 5.7 1.0 + - - -
213A ASN* 4.5 22.6 + - - +
216A LEU* 3.4 34.1 + - + +
217A SER* 5.7 1.8 + - - -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.1 24.2 - - + -
113A LEU* 4.3 10.1 - - + -
116A ALA* 3.9 9.4 - - + +
117A THR 3.0 19.0 + - - +
118A ALA* 3.6 9.9 - - - +
120A GLN* 1.3 74.5 - - - +
122A THR* 1.3 65.9 + - - +
124A ALA* 3.2 10.6 + - - +
125A VAL* 3.2 15.8 + - + +
369C PHE* 4.9 2.5 - - + -
371C LEU* 3.8 38.1 - - + +
418C LEU* 3.9 21.3 - - + -
420C PHE* 4.6 6.1 - - + -
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Residues in contact with THR 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 ALA 2.9 17.0 + - - -
119A ALA* 3.3 12.6 - - - +
121A VAL* 1.3 77.0 - - - +
123A ALA* 1.3 63.5 + - - +
125A VAL* 3.1 14.9 + - - +
126A ALA* 3.1 14.9 + - + +
365C PHE* 3.9 19.8 - - - -
366C LEU* 5.6 1.1 - - - +
418C LEU* 4.1 21.2 - - + +
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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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119A ALA 2.8 19.8 + - - +
120A GLN* 3.6 5.4 - - - +
122A THR* 1.3 75.4 - - - +
124A ALA* 1.3 57.2 + - - +
126A ALA* 3.4 3.1 + - - +
127A LEU* 3.0 23.4 + - - +
216A LEU* 4.2 24.4 - - + +
258A GLN* 3.3 32.5 - - + +
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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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90A ILE* 4.9 6.5 - - + -
95A ILE* 4.5 3.9 - - + +
110A LEU* 4.8 8.5 - - + -
113A LEU* 3.9 27.4 - - + -
120A GLN 2.9 16.7 + - - +
121A VAL 3.2 6.2 + - - +
123A ALA* 1.3 73.4 - - - +
125A VAL* 1.3 64.6 + - - +
127A LEU* 3.1 19.4 - - - +
128A VAL* 3.2 13.6 + - - +
216A LEU* 3.8 16.4 - - + -
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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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95A ILE* 5.8 0.2 - - - -
103A PHE* 5.7 0.2 - - + -
107A VAL* 3.8 40.4 - - + -
110A LEU* 5.2 0.9 - - + -
121A VAL* 3.2 16.4 + - + +
122A THR 3.1 7.9 + - - +
124A ALA* 1.3 77.0 - - + +
126A ALA* 1.3 65.0 + - - +
128A VAL* 2.9 26.9 - - + +
129A LYS* 3.0 32.9 + - + +
418C LEU* 4.0 24.2 - - + -
419C ARG 4.8 3.8 - - - +
420C PHE* 5.3 1.6 - - + -
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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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122A THR* 3.1 13.9 + - + +
123A ALA* 3.6 4.5 - - - +
125A VAL* 1.3 77.9 - - - +
127A LEU* 1.3 56.9 + - - +
129A LYS* 3.4 10.8 + - - +
130A ALA* 3.0 30.0 + - - +
258A GLN* 3.5 25.8 - - - +
260A VAL* 5.3 0.6 - - - +
272A LYS* 5.1 9.7 + - + +
274A GLU* 5.9 2.7 - - - +
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Residues in contact with LEU 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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87A LEU* 4.3 20.6 - - + -
90A ILE* 4.2 25.6 - - + -
91A ARG* 4.3 21.3 + - + -
123A ALA 3.0 14.1 + - - +
124A ALA* 3.1 11.4 - - - +
125A VAL 3.1 0.4 - - - -
126A ALA* 1.3 77.4 - - - +
128A VAL* 1.3 63.5 + - + +
130A ALA* 3.2 5.5 + - - +
131A ASN* 3.2 18.5 + - - +
215A ALA 5.5 0.2 - - - +
216A LEU* 4.7 11.7 - - + -
258A GLN* 4.4 6.3 + - - +
259A ILE 3.9 8.7 - - - +
260A VAL* 3.5 40.3 - - - +
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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
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91A ARG* 5.2 4.7 - - + -
95A ILE* 3.2 50.0 - - + -
96A PRO* 3.6 15.0 - - + -
103A PHE* 3.8 37.6 - - + +
107A VAL* 5.1 2.9 - - + -
124A ALA 3.2 3.5 + - - +
125A VAL* 2.9 27.4 - - + +
127A LEU* 1.3 77.5 - - + +
129A LYS* 1.3 65.3 + - - +
130A ALA 3.1 2.0 - - - -
131A ASN* 3.0 23.5 + - - +
132A GLU 4.6 0.5 + - - -
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Residues in contact with LYS 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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103A PHE* 4.0 23.8 - - + -
125A VAL* 3.0 38.5 + - + +
126A ALA* 3.6 9.4 - - - +
127A LEU 3.3 0.2 - - - -
128A VAL* 1.3 78.7 - - - +
130A ALA* 1.3 58.6 + - - +
131A ASN 3.3 0.2 - - - -
132A GLU* 4.7 3.3 + - - +
133A ASN* 4.4 8.1 + - - -
272A LYS* 5.9 2.9 - - - +
417C ASN 5.9 1.2 + - - -
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Residues in contact with ALA 130 (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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48A PHE* 4.1 19.0 - - + -
126A ALA 3.0 16.6 + - - +
127A LEU 3.7 5.2 - - - +
128A VAL 3.1 0.6 - - - -
129A LYS* 1.3 74.4 - - - +
131A ASN* 1.3 65.3 + - - +
132A GLU 3.2 3.1 - - - -
133A ASN* 3.0 11.1 + - - +
134A ALA* 3.0 22.1 + - - +
260A VAL* 4.0 25.1 - - + -
272A LYS* 4.5 9.6 - - + +
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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