Contacts of the helix formed by residues 105 - 118 (chain A) in PDB entry 2B7O
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLY 3.0 19.1 + - - +
102A ASN* 3.8 6.3 - - - +
103A VAL 3.3 0.2 - - - -
104A ARG* 1.3 76.2 - - - +
106A LEU* 1.3 57.2 + - - +
108A GLN* 3.3 11.7 + - - +
109A MSE 2.9 36.1 + - - +
412A ILE* 4.4 15.5 - - + -
413A THR 4.8 2.2 - - - +
414A GLY* 4.6 12.8 - - - +
446A THR* 5.4 3.6 - - - +
449A SER* 4.7 9.4 - - - +
450A LEU* 4.3 5.6 - - + +
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Residues in contact with LEU 106 (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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82A LEU* 3.6 28.0 - - + +
84A GLY* 3.7 35.9 - - - +
102A ASN 3.1 17.4 + - - +
103A VAL* 3.7 5.8 - - - +
104A ARG 3.2 0.2 - - - -
105A ALA* 1.3 77.9 - - - +
107A LEU* 1.3 55.2 + - - +
109A MSE 3.5 3.5 + - - +
110A ALA* 2.8 30.4 + - - +
123A LYS* 4.0 16.2 - - + -
124A VAL 4.1 2.0 - - - +
125A ALA* 4.0 18.2 - - + +
243A ILE* 3.8 33.0 - - + -
412A ILE* 4.5 9.4 - - + +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.0 36.6 + - + +
104A ARG* 3.6 9.4 - - - +
106A LEU* 1.3 75.0 - - - +
108A GLN* 1.3 63.0 + - - +
110A ALA* 3.1 5.7 + - + +
111A VAL* 3.0 21.1 + - - +
123A LYS* 3.8 29.2 - - + -
186A LEU 5.9 0.2 - - - +
187A THR* 5.3 1.8 - - + -
191A LEU* 3.7 26.9 - - + +
192A ALA* 4.0 15.0 - - + +
197A VAL* 3.6 20.5 - - + +
200A TRP* 5.2 0.2 - - + -
241A ALA* 4.1 14.8 - - + -
243A ILE* 4.1 12.3 - - + -
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Residues in contact with GLN 108 (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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104A ARG* 2.7 32.2 + - - +
105A ALA* 3.5 8.0 + - - +
107A LEU* 1.3 72.3 - - - +
109A MSE 1.3 61.8 + - - +
111A VAL* 3.3 17.3 - - - +
112A VAL* 3.4 6.0 + - - +
197A VAL* 3.5 10.3 - - - +
200A TRP* 3.6 46.4 + - + +
201A ASN* 2.6 38.1 + - - +
446A THR* 5.5 2.3 + - - -
450A LEU* 3.2 30.7 - - + +
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Residues in contact with MSE 109 (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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82A LEU* 3.8 35.0 - - + -
105A ALA 2.9 21.7 + - - +
106A LEU* 4.9 2.0 - - - -
108A GLN* 1.3 75.0 - - - +
110A ALA* 1.3 62.8 + - - +
112A VAL* 3.4 3.4 + - - +
113A LEU* 3.1 27.2 + - + +
408A ILE* 4.3 12.1 - - + -
410A VAL* 4.2 16.4 - - + -
412A ILE* 3.7 29.2 - - - -
449A SER* 3.4 34.3 - - - +
450A LEU* 4.2 12.6 - - + -
452A LEU* 5.0 3.1 - - + -
453A ALA* 3.8 21.5 - - + +
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Residues in contact with ALA 110 (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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82A LEU* 3.7 8.9 - - + +
106A LEU 2.8 20.7 + - - +
107A LEU* 3.1 5.6 + - + +
109A MSE 1.3 77.4 - - - +
111A VAL* 1.3 54.5 + - - +
113A LEU* 3.4 1.7 + - - +
114A THR* 2.5 38.5 + - - +
121A VAL* 4.0 10.0 - - + +
123A LYS* 3.5 33.2 - - + +
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Residues in contact with VAL 111 (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 LEU 3.0 14.6 + - - +
108A GLN 3.3 15.7 - - - +
110A ALA* 1.3 75.8 - - - +
112A VAL* 1.3 62.0 + - - +
114A THR* 3.7 7.1 - - - -
115A TYR* 3.2 22.5 + - - +
194A LEU* 4.3 28.7 - - + +
197A VAL* 3.9 13.7 - - + -
198A HIS* 4.4 7.4 - - + +
201A ASN* 3.5 16.4 - - - +
221A ILE* 4.3 18.1 - - + +
225A LEU* 4.7 16.4 - - + -
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Residues in contact with VAL 112 (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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108A GLN 3.6 5.4 - - - +
109A MSE 3.4 7.7 + - - +
110A ALA 3.3 0.4 - - - -
111A VAL* 1.3 76.8 - - - +
113A LEU* 1.3 56.6 + - - +
115A TYR* 3.4 5.2 + - - +
116A GLY 3.1 22.0 + - - -
201A ASN* 3.4 26.7 - - - +
217A LEU* 4.3 0.8 - - + +
221A ILE* 3.9 20.2 - - + +
450A LEU* 6.3 0.9 - - + -
453A ALA* 3.9 5.2 - - + +
454A PHE* 3.9 61.7 - - + +
457A ALA* 3.7 12.8 - - + +
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Residues in contact with LEU 113 (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 PHE* 4.2 17.3 - - + -
82A LEU* 4.0 35.2 - - + -
109A MSE 3.1 23.2 + - + +
110A ALA* 4.0 2.9 - - - +
112A VAL* 1.3 72.2 - - - +
114A THR* 1.3 62.3 + - - +
116A GLY 4.4 0.4 - - - +
117A ALA* 2.8 34.3 + - - +
121A VAL* 3.9 10.1 - - + -
408A ILE* 4.5 6.5 - - + -
453A ALA* 3.7 30.3 - - + +
456A VAL* 3.8 28.3 - - + -
457A ALA* 3.9 7.6 - - - +
460A LEU* 4.0 7.2 - - + +
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Residues in contact with THR 114 (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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110A ALA* 2.5 25.7 + - - +
111A VAL* 3.7 8.6 - - - -
112A VAL 3.3 0.2 - - - -
113A LEU* 1.3 75.0 - - - +
115A TYR* 1.3 57.8 + - - +
118A SER* 2.8 29.6 + - - -
119A MSE 3.4 21.8 + - - +
120A PRO* 4.6 5.4 - - + -
121A VAL* 3.4 20.5 + - - +
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Residues in contact with TYR 115 (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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111A VAL 3.2 11.2 + - - +
112A VAL 3.6 7.9 - - - +
114A THR* 1.3 80.6 - - - +
116A GLY* 1.3 62.0 + - - +
118A SER* 3.4 15.6 + - - +
217A LEU* 3.7 21.1 - - + -
220A GLU* 2.5 57.2 + - + +
221A ILE* 3.7 24.7 - - + -
224A GLY* 4.7 11.8 - - - -
461A ARG* 3.4 13.9 + - - -
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Residues in contact with GLY 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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112A VAL 3.1 11.1 + - - -
113A LEU 3.9 1.6 - - - -
115A TYR* 1.3 81.4 - - - +
117A ALA* 1.3 60.6 + - - +
118A SER* 4.3 2.9 + - - -
217A LEU* 5.7 0.2 - - - -
457A ALA* 3.8 27.4 - - - -
460A LEU* 3.7 8.8 - - - +
461A ARG* 3.6 32.5 + - - +
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Residues in contact with ALA 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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80A PHE* 4.6 10.5 - - + -
113A LEU 2.8 22.5 + - - +
114A THR 4.1 1.1 - - - +
116A GLY* 1.3 72.1 - - - +
118A SER* 1.3 70.1 + - - +
119A MSE 3.5 35.9 + - + +
121A VAL* 5.2 0.2 - - + -
460A LEU* 3.7 31.7 - - + +
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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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114A THR 2.8 14.7 + - - -
115A TYR* 3.4 12.1 + - - +
116A GLY 3.4 3.6 + - - -
117A ALA* 1.3 79.0 - - - +
119A MSE 1.3 60.0 + - - +
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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