Contacts of the strand formed by residues 128 - 139 (chain A) in PDB entry 1BGB
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 TYR 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PRO* 3.6 8.2 - - + +
76A THR* 3.1 39.0 + - + -
86A LYS* 3.2 17.0 - - + +
87A ILE 3.8 1.8 - - - -
88A ALA* 3.7 28.0 - - + -
121A ILE* 3.4 16.6 - - + +
122A VAL* 3.5 6.1 - - - +
123A TYR* 3.2 52.9 + - + -
124A PRO 3.9 4.5 - - - -
125A PHE 3.4 16.0 + - - +
126A ASP* 3.2 9.4 - - - +
127A GLN* 1.3 79.4 - - - +
129A ILE* 1.3 64.2 + - - +
130A ALA 4.1 2.2 - - - +
131A HIS* 3.5 28.3 + + + +
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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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84A ASN 4.5 3.8 - - - +
85A LYS* 3.8 36.8 - - + +
86A LYS 2.7 17.3 + - - +
87A ILE* 4.8 7.6 - - + -
126A ASP 5.5 2.0 - - - +
127A GLN 4.0 0.2 + - - -
128A TYR* 1.3 77.3 - - - +
130A ALA* 1.3 67.0 + - + +
131A HIS* 5.0 3.6 - - - -
209A GLU* 4.8 11.0 - - - +
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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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86A LYS 3.5 2.5 + - - +
87A ILE* 3.5 22.0 - - + -
88A ALA* 2.8 31.0 + - - +
128A TYR* 3.6 2.0 - - - +
129A ILE* 1.3 86.2 - - + +
131A HIS* 1.3 65.8 + - - +
132A TRP* 3.9 24.2 - - + +
172A ASP* 4.7 3.6 - - - +
209A GLU* 5.5 1.1 - - - -
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Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.1 29.6 + + - +
88A ALA* 3.4 10.9 - - + +
125A PHE* 3.6 41.2 + + - -
128A TYR* 3.5 39.5 + + + +
129A ILE 5.0 1.1 - - - -
130A ALA* 1.3 76.8 - - - +
132A TRP* 1.3 61.9 + - - +
133A ILE* 5.5 0.9 - - - -
172A ASP* 3.5 7.5 + - - +
173A LYS* 2.8 46.3 + - + +
209A GLU* 4.0 21.2 + - - +
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Residues in contact with TRP 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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3A LEU* 4.2 23.3 - - + -
4A ARG* 3.5 54.3 - - + +
7A LEU* 4.2 14.6 - - + -
72A TYR* 5.6 0.7 + - - -
87A ILE* 3.9 28.5 - - + -
88A ALA 2.7 12.2 + - - +
89A ILE* 3.3 20.0 - - + -
90A ASP* 2.9 25.3 + - - +
130A ALA* 3.9 10.3 - - + +
131A HIS* 1.3 80.5 - - - +
133A ILE* 1.3 64.7 + - - +
134A ILE 4.2 0.2 - - - -
170A LEU* 3.9 28.0 - - + -
171A GLN 3.5 3.6 - - - +
172A ASP* 3.0 32.9 + - - -
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Residues in contact with ILE 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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72A TYR* 5.6 0.4 - - - +
90A ASP* 3.2 26.9 - - + +
92A LYS* 4.1 26.0 - - + -
105A PHE* 5.8 1.6 - - + -
107A LEU* 3.9 21.5 - - + -
132A TRP* 1.3 78.2 - - - +
134A ILE* 1.3 76.3 + - - +
135A GLY* 3.6 6.0 + - - +
169A PHE* 3.6 5.5 - - + +
170A LEU* 3.3 4.0 - - - -
171A GLN 2.8 32.3 + - - +
173A LYS* 3.9 41.7 - - + -
176A ILE* 4.3 16.2 - - + -
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Residues in contact with ILE 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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7A LEU* 4.6 2.9 - - + -
11A LEU* 3.8 30.5 - - + -
52A ILE* 3.9 19.3 - - + -
89A ILE* 3.5 27.8 - - + -
90A ASP 2.8 10.9 + - - +
91A ILE* 3.2 14.8 - - + +
92A LYS 2.8 31.0 + - - +
133A ILE* 1.3 75.2 - - - +
135A GLY* 1.3 53.4 + - - +
136A TYR* 3.8 13.7 - - + -
168A VAL* 3.5 28.3 - - + -
169A PHE 3.3 4.7 - - - +
170A LEU* 3.8 22.2 - - + -
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Residues in contact with GLY 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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92A LYS 3.2 7.0 - - - -
105A PHE* 4.1 4.7 - - - -
133A ILE* 3.6 8.2 + - - +
134A ILE* 1.3 74.2 - - - +
136A TYR* 1.3 61.4 + - - -
168A VAL* 3.1 8.1 - - - +
169A PHE* 3.0 59.0 + - - -
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Residues in contact with TYR 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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11A LEU* 3.7 12.0 + - - +
15A ASN* 4.3 11.7 - - - -
44A PHE* 3.8 41.5 - + + -
47A PHE* 3.5 16.6 - + - -
48A SER* 2.5 29.4 + - - -
91A ILE* 3.6 28.3 - - + -
92A LYS 2.8 6.0 + - - +
93A THR* 3.3 14.8 - - - +
94A THR 3.1 24.9 + - - -
105A PHE* 3.8 2.8 - - - -
134A ILE* 3.8 13.7 - - + -
135A GLY* 1.3 76.7 - - - -
137A VAL* 1.3 65.2 + - - +
166A VAL* 4.1 10.8 - - + -
167A LYS 3.3 3.1 - - - -
168A VAL* 3.7 27.2 - - + +
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Residues in contact with VAL 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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94A THR* 3.4 8.1 - - + +
95A TYR 4.8 0.2 - - - -
96A THR* 4.5 15.0 - - + -
99A GLU* 5.8 1.6 - - - +
103A ILE* 3.4 50.5 - - + -
105A PHE* 3.9 10.1 - - + -
136A TYR* 1.3 80.5 - - - +
138A TYR* 1.3 61.6 + - - +
165A GLY 3.9 2.5 - - - +
166A VAL* 3.4 4.5 - - - +
167A LYS* 2.9 47.0 + - + +
169A PHE* 4.5 3.6 - - + -
196A TYR* 4.3 15.7 - - + -
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Residues in contact with TYR 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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35A SER 3.6 16.2 + - - -
37A THR* 2.9 28.7 + - - -
40A LEU* 3.7 39.0 - - + -
44A PHE* 3.9 20.6 - + + -
93A THR* 3.9 16.4 - - + -
94A THR 3.1 29.8 + - - -
95A TYR* 3.0 29.5 - - + +
96A THR* 2.7 35.9 + - - +
137A VAL* 1.3 75.6 - - - +
139A THR* 1.3 63.6 + - - +
140A ARG* 4.2 17.1 - - + +
162A PRO 4.7 1.1 - - - -
163A TYR* 3.9 5.6 - - + -
164A LYS 4.0 4.5 - - - -
165A GLY 4.6 1.3 - - - -
166A VAL* 4.1 10.1 - - + +
69B GLN* 4.4 4.0 + - - -
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Residues in contact with THR 139 (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 THR* 2.8 30.8 - - - +
97A ASN 3.4 21.1 - - - +
98A LYS 5.3 0.9 - - - -
99A GLU* 3.8 20.8 + - - +
138A TYR* 1.3 74.3 - - - +
140A ARG* 1.3 69.5 + - - +
141A VAL* 3.6 0.6 + - - -
163A TYR* 3.1 8.3 - - - -
164A LYS* 2.9 49.4 + - + +
165A GLY 4.6 0.3 + - - -
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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