Contacts of the strand formed by residues 189 - 197 (chain A) in PDB entry 3EBL
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 GLN 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A MET* 6.5 0.2 - - - -
183A ARG* 3.6 15.0 - - - +
184A SER* 3.0 25.5 + - - +
187A ASP* 3.0 24.3 + - - +
188A ALA* 1.3 76.9 - - - +
190A ALA* 1.3 68.2 + - - +
191A ARG* 3.4 7.9 + - + +
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Residues in contact with ALA 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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115A VAL* 5.1 0.7 - - + -
176A VAL* 4.3 6.5 - - + +
177A MET* 3.9 34.7 + - - +
182A MET* 3.6 25.6 - - + +
183A ARG* 3.6 8.2 - - + +
189A GLN* 1.3 75.9 - - - +
191A ARG* 1.3 60.8 + - - +
192A VAL* 3.3 26.0 + - + +
217A LYS 5.0 2.1 - - - +
219A CYS* 5.2 0.7 - - - -
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Residues in contact with ARG 191 (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 PRO* 3.8 22.5 - - - +
113A PHE 3.7 10.7 + - - +
114A PRO* 3.6 3.6 - - - +
115A VAL* 3.0 24.4 + - - +
182A MET 4.4 3.4 + - - -
184A SER* 3.0 45.1 + - - -
185A GLY* 3.4 15.6 - - - -
186A GLY 3.8 1.8 - - - +
187A ASP* 2.7 31.8 + - - -
189A GLN* 3.4 4.6 + - + +
190A ALA* 1.3 70.3 - - - +
192A VAL* 1.3 61.8 + - - +
193A PHE* 3.8 2.9 - - - -
219A CYS* 3.8 19.3 - - - -
352A LEU* 2.9 42.1 + - + +
353A TYR* 4.4 8.1 + - - +
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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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115A VAL* 3.4 6.7 - - + +
117A ILE* 3.6 27.1 - - + -
173A LEU* 3.8 13.5 - - + -
176A VAL* 4.0 15.5 - - + -
177A MET* 3.7 34.3 - - + -
190A ALA* 3.3 17.0 + - + +
191A ARG* 1.3 72.1 - - - +
193A PHE* 1.3 71.7 + - - +
194A LEU* 4.2 7.0 - - + -
217A LYS 4.8 4.4 + - - +
218A VAL* 3.7 5.3 - - + +
219A CYS* 2.8 37.1 + - - +
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Residues in contact with PHE 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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114A PRO* 4.0 16.8 - - + -
115A VAL 2.8 10.1 + - - +
116A ILE* 3.5 6.9 - - + -
117A ILE* 2.8 27.4 + - - -
191A ARG 3.8 9.9 - - - -
192A VAL* 1.3 82.2 - - - +
194A LEU* 1.3 60.5 + - - +
219A CYS* 3.7 15.3 - - + -
220A GLY* 3.1 24.5 - - - +
222A ILE* 4.2 10.5 - - + -
347A PHE* 3.8 21.1 - + - -
348A LEU* 3.5 45.1 - - + -
351A ASN* 3.7 33.9 - - + -
352A LEU* 4.5 9.4 - - + -
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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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117A ILE* 3.6 34.1 - - + -
119A PHE* 4.3 8.5 - - + -
173A LEU* 4.5 5.8 - - + -
192A VAL* 4.2 5.2 - - + -
193A PHE* 1.3 74.0 - - - +
195A SER* 1.3 53.2 + - - +
204A ALA* 3.8 18.3 - - + +
207A VAL* 3.9 21.8 - - + -
208A ALA* 3.6 36.6 - - - +
218A VAL* 3.8 22.2 - - + -
220A GLY 3.0 6.5 + - - -
221A ASN* 3.1 18.5 - - - +
222A ILE* 2.7 30.8 + - - +
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Residues in contact with SER 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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116A ILE* 3.8 26.2 - - - -
117A ILE 2.8 13.1 + - - +
118A PHE* 4.0 11.3 - - - -
119A PHE* 2.9 27.8 + - - -
141A PHE* 4.2 5.5 - - - -
194A LEU* 1.3 76.0 - - - +
196A GLY* 1.3 59.0 + - - +
204A ALA* 4.1 7.1 - - - +
222A ILE* 2.9 35.8 + - - +
224A LEU* 4.0 6.9 - - - +
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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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118A PHE* 3.8 5.8 - - - -
119A PHE 3.2 15.5 - - - -
195A SER* 1.3 80.2 + - - +
197A ASP* 1.3 59.3 + - - -
200A GLY 3.6 10.2 + - - -
201A GLY* 3.4 16.9 - - - -
204A ALA* 4.4 0.4 - - - +
222A ILE 3.1 3.3 + - - +
223A LEU* 3.6 1.6 - - - -
224A LEU* 2.9 27.0 + - - -
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Residues in contact with ASP 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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118A PHE* 3.5 10.1 - - + -
119A PHE 3.5 0.6 + - - -
121A GLY* 2.8 23.7 + - - -
134A TYR* 2.7 37.6 + - - -
196A GLY* 1.3 73.5 - - - -
198A SER* 1.3 72.0 + - - +
200A GLY* 2.8 13.9 + - - -
201A GLY 3.6 0.2 - - - -
224A LEU* 3.0 18.4 - - + +
329A TYR* 2.5 39.9 + - + +
401A GA4 3.4 3.8 - - - +
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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