Contacts of the helix formed by residues 130 - 138 (chain A) in PDB entry 4BBZ
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 GLY 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A TRP* 3.5 29.0 - - - +
128A TYR 3.2 6.6 + - - -
129A ASP* 1.3 71.6 + - - +
131A LYS* 1.3 63.5 + - - +
132A PHE 3.3 3.5 + - - -
133A LEU* 3.5 3.9 + - - -
134A ALA* 3.2 19.9 + - - +
141A VAL* 3.6 24.4 - - - +
446A PHE* 4.3 5.6 - - - -
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.0 22.4 - - + +
19A THR 5.6 2.2 + - - -
20A VAL* 3.8 25.9 - - + +
25A VAL* 3.5 11.6 - - + +
98A TRP* 3.7 21.5 - - + -
129A ASP* 3.3 30.6 + - - +
130A GLY* 1.3 76.9 - - - +
132A PHE* 1.3 86.5 + - + +
134A ALA 3.5 0.2 + - - -
135A ARG* 3.0 29.6 + - - +
451A GLU* 5.9 0.6 + - - -
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Residues in contact with PHE 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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20A VAL* 3.8 13.5 - - + -
21A PHE* 3.4 35.9 - + + -
126A HIS* 5.9 4.9 - + - -
129A ASP* 4.1 12.1 - - + -
130A GLY 3.3 0.8 - - - -
131A LYS* 1.3 101.2 - - + +
133A LEU* 1.3 60.2 + - - +
135A ARG* 3.3 4.7 + - - +
136A VAL* 2.9 36.3 + - + +
446A PHE 3.4 24.0 - - - +
447A GLY* 3.8 12.6 - - - +
448A LEU* 3.4 29.2 - - + -
450A LEU* 5.2 1.3 - - + -
451A GLU* 4.1 26.2 - - + -
468A VAL* 6.2 0.2 - - - -
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Residues in contact with LEU 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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110A LEU* 4.6 14.6 - - + -
130A GLY* 3.5 3.6 + - - +
131A LYS 3.4 0.2 - - - -
132A PHE* 1.3 75.0 - - - +
134A ALA* 1.3 66.8 + - - +
136A VAL* 5.0 1.8 - - - -
137A GLU* 3.0 27.5 + - + +
138A ARG 3.5 4.2 + - - -
139A VAL* 3.7 10.3 - - + +
141A VAL* 3.7 22.0 - - + -
195A PHE* 4.6 13.9 - - + -
445A VAL* 3.7 23.1 - - + +
446A PHE* 3.9 36.3 + - + +
468A VAL* 3.7 33.2 - - + +
471A TRP* 5.6 4.5 - - + -
472A ALA* 5.6 1.3 - - + -
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Residues in contact with ALA 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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25A VAL* 4.1 12.8 - - + -
98A TRP* 4.1 19.3 - - + +
100A PRO* 3.6 20.7 - - - +
130A GLY 3.2 15.0 + - - +
131A LYS 3.8 3.8 - - - +
132A PHE 3.3 0.2 - - - -
133A LEU* 1.3 77.6 - - - +
135A ARG* 1.3 64.1 + - - +
138A ARG* 3.0 23.2 + - - -
139A VAL 3.2 20.9 - - - +
141A VAL* 4.3 1.7 - - + +
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Residues in contact with ARG 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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20A VAL* 2.8 36.7 + - + +
21A PHE* 2.8 38.1 + - + +
22A GLY 3.9 3.6 + - - -
23A GLY* 3.3 19.8 - - - +
24A THR 4.2 8.5 - - - +
25A VAL* 3.6 12.9 - - + +
100A PRO* 5.3 2.2 - - - +
131A LYS 3.0 18.2 + - - +
132A PHE 3.5 3.6 - - - +
134A ALA* 1.3 79.8 - - - +
136A VAL* 1.3 63.1 + - + +
138A ARG* 4.3 10.0 + - - +
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Residues in contact with VAL 136 (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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21A PHE* 3.7 33.7 - - + -
132A PHE 2.9 23.1 + - - +
135A ARG* 1.3 76.3 - - + +
137A GLU* 1.3 68.2 + - + +
138A ARG* 5.3 1.1 - - - +
450A LEU* 4.2 14.6 - - + -
465A ARG* 3.5 45.2 + - - +
468A VAL* 4.6 4.0 - - + -
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Residues in contact with GLU 137 (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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133A LEU* 3.0 14.6 + - + +
136A VAL* 1.3 81.5 - - + +
138A ARG* 1.3 70.2 + - - +
139A VAL* 3.1 9.4 + - + +
465A ARG* 2.8 27.6 + - - -
468A VAL* 3.5 23.6 - - + -
469A LYS* 2.8 39.5 + - - -
472A ALA* 3.8 26.0 - - + +
476A LYS* 2.9 36.8 + - - +
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Residues in contact with ARG 138 (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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100A PRO* 3.7 27.0 - - + +
101A ALA 4.1 12.3 + - - -
102A PRO* 3.4 34.9 + - - +
103A LYS 4.6 1.0 + - - -
104A PRO* 3.8 20.5 - - + +
107A ALA* 3.8 14.4 - - - +
108A THR 5.3 0.2 + - - -
133A LEU 3.5 0.2 + - - -
134A ALA 3.0 21.1 + - - +
135A ARG 4.4 8.5 - - - +
136A VAL 5.3 0.9 - - - +
137A GLU* 1.3 79.7 - - - +
139A VAL* 1.3 62.1 + - - +
476A LYS* 5.3 1.4 - - - -
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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