Contacts of the strand formed by residues 187 - 197 (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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A LYS 5.1 0.7 - - - +
106A ASN* 4.3 4.9 - - - +
107A ALA 3.6 8.5 - - - -
109A VAL* 4.2 0.7 - - - -
140A ILE* 3.7 12.1 - - - -
182A ILE* 2.6 32.7 + - - -
183A ALA* 3.2 20.3 - - - +
185A PHE 3.3 1.6 - - - -
186A GLY* 1.3 75.3 - - - +
188A ASN* 1.3 60.6 + - - -
189A PRO* 3.4 4.5 - - - +
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Residues in contact with ASN 188 (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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106A ASN* 3.6 30.0 + - - +
107A ALA 2.8 18.0 + - - +
109A VAL* 4.0 2.5 - - - +
182A ILE* 4.2 2.9 - - - -
187A GLY* 1.3 71.4 - - - -
189A PRO* 1.3 60.9 - - - +
190A LYS* 3.0 20.5 + - - +
191A SER* 2.7 52.5 + - - +
192A VAL* 3.9 2.4 - - - +
550A NAG 3.3 35.8 + - - +
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Residues in contact with PRO 189 (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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106A ASN* 5.3 1.1 - - - +
178A VAL 5.1 0.2 - - - +
179A GLN* 2.9 62.0 + - - +
182A ILE* 3.8 12.0 - - + -
183A ALA* 4.5 11.9 - - + -
187A GLY 3.4 10.3 - - - +
188A ASN* 1.3 88.8 - - - +
190A LYS* 1.3 64.2 + - + +
191A SER 3.2 0.7 - - - -
192A VAL* 3.3 14.1 - - + +
217A PHE* 5.7 1.0 - - - -
218A THR* 4.9 0.9 + - - -
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Residues in contact with LYS 190 (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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188A ASN* 3.0 13.0 + - - +
189A PRO* 1.3 82.9 - - + +
191A SER* 1.3 59.4 + - - +
218A THR* 3.1 20.1 + - - +
550A NAG 3.7 42.1 + - - +
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A THR* 2.9 32.3 + - - +
109A VAL 2.8 30.3 + - - -
188A ASN* 2.7 30.8 + - - +
190A LYS* 1.3 80.4 - - - +
192A VAL* 1.3 52.8 + - - +
193A THR* 4.2 0.7 - - - -
218A THR* 3.7 4.5 - - - -
219A ARG* 4.4 5.4 + - - +
475A ALA 3.9 9.1 + - - -
476A LYS 4.5 3.3 + - - -
550A NAG 5.6 0.4 - - - -
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Residues in contact with VAL 192 (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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109A VAL* 3.3 13.2 - - + +
111A ILE* 3.5 37.0 - - + -
178A VAL* 4.3 8.5 - - + -
179A GLN* 3.8 11.2 - - - +
188A ASN 3.9 4.0 - - - +
189A PRO* 3.3 27.6 - - + +
191A SER* 1.3 76.9 - - - +
193A THR* 1.3 64.1 + - - +
194A LEU* 4.4 1.8 - - + -
216A LEU 4.3 9.2 - - - +
217A PHE* 3.8 17.1 - - + +
218A THR* 2.9 38.4 + - - -
219A ARG 3.3 0.9 + - - -
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Residues in contact with THR 193 (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 THR* 4.8 0.7 - - - +
109A VAL 2.8 9.3 + - - -
110A LEU* 3.5 21.7 - - + +
111A ILE 2.9 23.9 + - - -
191A SER 4.2 0.2 - - - -
192A VAL* 1.3 77.0 + - - +
194A LEU* 1.3 75.2 + - - +
195A PHE 3.6 0.7 + - - -
218A THR* 5.4 0.5 - - - -
219A ARG* 3.5 21.4 - - - +
220A ALA 4.3 0.2 - - - +
221A ILE* 3.9 27.8 - - + -
474A PHE* 4.3 4.3 - - + -
475A ALA* 3.2 30.3 + - + +
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Residues in contact with LEU 194 (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 ILE* 3.6 21.5 - - + +
113A ILE* 5.1 4.0 - - + -
175A LEU* 3.6 35.4 - - + -
192A VAL* 4.1 1.1 - - + -
193A THR* 1.3 77.4 - - - +
195A PHE* 1.3 59.7 + - - +
204A VAL* 3.9 22.0 - - + +
207A HIS* 3.9 22.9 - - + -
217A PHE* 3.5 53.8 - - + -
219A ARG 3.1 7.2 + - - +
220A ALA* 3.4 2.4 - - - -
221A ILE 2.9 23.9 + - - +
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Residues in contact with PHE 195 (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* 3.8 30.1 - - + -
111A ILE 2.9 24.9 + - - +
112A TRP* 3.2 53.2 - + + -
113A ILE* 2.9 23.4 + - - +
133A LEU* 4.6 10.5 - - + -
141A VAL* 4.7 3.4 - - + -
193A THR 4.3 0.9 - - - -
194A LEU* 1.3 76.3 - - - +
196A GLY* 1.3 59.3 - - - +
204A VAL* 4.0 5.4 - - - -
221A ILE* 3.4 30.5 - - + -
223A GLN* 4.0 9.6 - - - +
445A VAL* 4.1 15.0 - - + -
446A PHE* 3.7 21.1 - + - -
471A TRP* 4.3 11.7 - + - -
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Residues in contact with GLY 196 (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 TRP* 3.7 11.7 - - - -
113A ILE 3.1 15.9 - - - -
195A PHE* 1.3 76.8 - - - +
197A GLU* 1.3 60.4 + - - -
200A GLY 4.0 4.3 - - - -
201A ALA* 3.4 14.4 - - - +
204A VAL* 4.0 1.2 - - - +
221A ILE 3.5 5.3 + - - +
223A GLN* 2.9 28.6 + - - +
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Residues in contact with GLU 197 (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 TRP* 3.7 21.3 - - + -
113A ILE 3.5 4.8 + - - -
115A GLY* 3.2 15.1 + - - +
128A TYR* 5.2 0.7 + - - -
196A GLY* 1.3 75.3 - - - +
198A SER* 1.3 72.7 + - - +
200A GLY 2.8 15.1 + - - -
201A ALA 3.3 3.8 - - - +
223A GLN* 3.1 14.1 - - + +
224A SER* 4.2 2.4 - - - -
438A HIS* 3.4 20.1 + - - -
439A GLY* 3.3 22.2 + - - -
441A GLU* 3.3 23.3 - - - +
442A ILE* 3.6 17.3 - - + +
712A UNX 3.5 13.6 - - - -
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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