Contacts of the strand formed by residues 213 - 224 (chain A) in PDB entry 4BEI
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 ILE 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A THR* 3.9 28.9 - - + +
206A ALA 3.7 2.7 - - - -
207A VAL* 4.5 6.1 - - + +
211A GLY 4.1 9.9 - - - +
212A LEU* 1.3 77.8 - - - +
214A ILE* 1.3 57.4 + - - +
77B TRP* 3.2 8.1 + - - -
79B SER* 2.6 47.5 + - - -
80B ILE 4.6 6.5 - - - +
81B LYS* 3.9 24.0 - - + -
87B TYR* 3.9 36.6 - - + -
88B PHE 5.3 0.2 - - - +
132B SER* 5.4 5.2 - - - -
134B GLN* 2.9 14.7 + - - +
1272B O4B 4.7 7.2 - - - +
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Residues in contact with ILE 214 (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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205A THR* 3.2 3.9 - - - -
206A ALA* 2.7 49.2 + - + +
212A LEU* 4.3 15.7 - - + -
213A ILE* 1.3 71.6 - - - +
215A PRO* 1.3 81.7 - - + +
216A VAL* 3.6 0.5 - - - +
236A ILE* 4.7 10.3 - - + -
242A TYR* 3.9 34.3 - - + +
247A TYR* 3.7 30.5 - - + -
77B TRP* 3.5 33.4 - - + +
101B GLN* 4.9 2.2 - - + +
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Residues in contact with PRO 215 (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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204A MET 4.0 5.4 - - - +
205A THR* 4.6 1.8 - - + -
213A ILE 3.4 8.5 - - - +
214A ILE* 1.3 94.6 - - + +
216A VAL* 1.3 58.9 + - - +
217A ASN 5.1 2.2 - - - +
218A ALA* 5.6 1.1 - - - +
236A ILE* 5.6 0.3 - - - +
77B TRP* 3.4 34.5 - - + -
78B LEU 4.5 3.6 - - - +
79B SER* 3.7 11.2 - - - +
89B PRO* 3.8 28.3 - - + -
91B LYS* 6.2 3.4 - - + -
101B GLN* 3.9 17.1 - - - +
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Residues in contact with VAL 216 (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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186A PHE* 5.6 0.9 - - + -
204A MET* 2.9 40.9 + - + +
205A THR 3.7 2.9 - - - +
206A ALA* 3.6 25.4 - - + +
214A ILE 3.6 13.5 - - - +
215A PRO* 1.3 74.9 - - - +
217A ASN* 1.3 59.8 - - - +
234A ARG* 2.9 39.5 + - + +
235A GLY 4.5 5.0 - - - +
236A ILE* 4.0 33.0 - - + -
249A ILE* 4.9 4.9 - - + -
97B ASP* 4.6 0.4 - - - -
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Residues in contact with ASN 217 (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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202A PHE* 3.7 15.1 - - - -
203A TRP* 3.5 0.5 - - - +
204A MET* 2.9 49.8 + - + +
215A PRO* 5.3 0.7 - - - -
216A VAL* 1.3 79.8 - - - +
218A ALA* 1.3 89.3 + - - +
220A GLU* 3.1 16.9 + - - +
232A LYS* 3.0 38.4 - - - +
234A ARG* 3.6 14.7 - - - +
89B PRO* 3.4 9.2 - - - +
97B ASP* 3.5 6.7 - - - +
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Residues in contact with ALA 218 (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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202A PHE 3.4 3.6 - - - +
215A PRO* 5.6 2.3 - - - +
217A ASN* 1.3 91.2 + - - +
219A ARG* 1.3 67.2 + - - +
220A GLU* 3.2 4.7 + - - +
89B PRO* 4.2 7.4 - - - -
91B LYS* 3.5 34.3 - - + +
93B VAL* 4.0 15.0 - - + -
97B ASP* 2.7 28.7 + - + +
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Residues in contact with ARG 219 (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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201A GLU* 3.8 23.6 + - - +
202A PHE 3.5 4.3 - - - -
203A TRP* 3.6 31.4 - - + -
218A ALA* 1.3 68.5 - - - +
220A GLU* 1.3 59.8 + - - +
221A LYS* 4.3 1.4 + - - +
88B PHE* 3.4 33.1 - - - -
89B PRO* 2.8 26.4 + - + +
90B ALA* 2.9 24.9 + - - +
91B LYS 3.0 13.6 + - - +
92B ALA* 3.3 15.4 - - + +
93B VAL 2.9 28.9 + - - +
118B PHE* 4.0 5.3 - - - +
119B TRP* 2.4 38.2 + - - +
121B PRO* 3.5 20.4 - - - +
124B MET* 5.3 2.0 - - - +
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Residues in contact with GLU 220 (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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200A VAL 3.9 0.3 - - - +
201A GLU* 3.2 3.6 - - - -
202A PHE* 2.8 45.9 + - + +
217A ASN* 3.1 16.3 - - - +
218A ALA 3.7 10.8 - - - +
219A ARG* 1.3 73.1 - - - +
221A LYS* 1.3 62.9 + - - +
222A TRP* 2.7 31.1 + - + +
230A TYR* 2.5 24.9 + - - -
232A LYS* 3.2 9.9 + - - -
93B VAL* 3.6 13.9 - - + -
95B GLY 3.5 20.3 - - - +
97B ASP 2.7 23.0 + - - -
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Residues in contact with LYS 221 (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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200A VAL 3.5 4.5 - - - -
201A GLU* 4.0 15.8 + - - +
219A ARG 5.6 1.1 - - - +
220A GLU* 1.3 73.2 - - - +
222A TRP* 1.3 74.1 + - - +
256A ILE* 3.8 21.3 - - + -
93B VAL 4.2 6.0 + - - +
94B VAL* 4.0 13.0 + - - +
121B PRO* 5.6 3.2 - - - +
123B TYR* 3.5 27.8 + - - +
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Residues in contact with TRP 222 (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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190A LEU* 5.9 0.9 - - + -
198A ALA 3.5 1.7 - - - +
199A ASN* 3.4 4.9 - - - +
200A VAL* 2.8 50.4 + - + +
202A PHE* 5.3 5.4 - - + -
220A GLU* 2.7 36.6 + - + +
221A LYS* 1.3 87.6 - - - +
223A VAL* 1.3 72.7 + - - +
224A ILE* 3.9 13.0 + - + -
230A TYR* 3.6 41.4 - + - -
256A ILE* 5.2 1.3 - - - +
94B VAL 4.5 4.5 - - - -
95B GLY* 3.6 24.2 - - - -
96B VAL* 3.8 14.6 - - + -
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Residues in contact with VAL 223 (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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197A GLU* 3.5 37.9 - - + +
198A ALA 3.6 4.9 - - - +
199A ASN* 3.3 20.0 - - - +
222A TRP* 1.3 83.8 - - - +
224A ILE* 1.3 63.9 + - - +
225A ALA* 4.0 2.5 + - + +
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Residues in contact with ILE 224 (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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164A LEU* 4.4 10.5 - - + -
190A LEU* 4.2 17.9 - - + +
192A ASN* 2.8 33.0 + - + +
197A GLU* 3.5 2.2 - - - -
198A ALA* 2.9 30.3 + - + +
200A VAL* 4.1 21.8 - - + -
222A TRP* 4.2 13.0 - - + -
223A VAL* 1.3 76.3 - - - +
225A ALA* 1.3 70.6 + - - +
228A ASP* 3.6 27.4 - - + +
229A THR 4.4 1.6 - - - +
230A TYR* 4.1 27.4 - - + +
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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