Contacts of the strand formed by residues 213 - 224 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A TRP* 3.2 9.7 + - - -
79A SER* 2.7 47.5 + - - +
80A ILE 4.6 4.7 - - - +
81A LYS* 3.9 20.0 - - + -
87A TYR* 3.9 38.1 - - + -
88A PHE 5.3 0.7 - - - +
132A SER* 5.3 4.7 - - - -
134A GLN* 2.9 16.5 + - - +
1272A O4B 4.4 15.3 - - - +
205B THR* 4.0 27.1 - - + -
206B ALA 3.7 3.1 - - - -
207B VAL* 4.5 5.4 - - + +
211B GLY 3.5 4.0 + - - +
212B LEU* 1.3 77.6 - - - +
214B ILE* 1.3 60.3 + - - +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TRP* 3.6 26.9 - - + +
101A GLN* 4.9 3.1 - - + +
205B THR* 3.3 3.6 - - - -
206B ALA* 2.7 50.0 + - + +
212B LEU* 4.3 14.8 - - + -
213B ILE* 1.3 72.9 - - - +
215B PRO* 1.3 79.9 - - + +
216B VAL* 3.3 0.9 + - - +
236B ILE* 4.7 11.7 - - + -
242B TYR* 3.9 39.5 - - + +
247B TYR* 3.8 31.4 - - + -
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Residues in contact with PRO 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TRP* 3.5 33.4 - - + -
78A LEU 4.7 2.7 - - - +
79A SER* 3.9 11.6 - - - +
89A PRO* 3.9 27.6 - - + -
91A LYS* 6.3 3.4 - - + -
101A GLN* 3.9 17.1 - - - +
204B MET 4.0 5.6 - - - +
205B THR* 4.6 1.8 - - + -
213B ILE 3.4 9.0 - - - +
214B ILE* 1.3 93.9 - - + +
216B VAL* 1.3 59.4 - - - +
217B ASN 5.1 2.5 - - - +
218B ALA* 5.7 1.1 - - - +
236B ILE* 5.6 0.5 - - - +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 4.5 0.2 - - - -
186B PHE* 5.6 0.7 - - + -
204B MET* 2.9 40.1 + - + +
205B THR 3.7 3.4 - - - +
206B ALA* 3.6 25.4 - - + +
214B ILE 3.6 13.5 - - - +
215B PRO* 1.3 75.0 - - - +
217B ASN* 1.3 59.4 + - - +
234B ARG* 2.9 40.9 + - + +
235B GLY 4.6 5.4 - - - +
236B ILE* 4.0 33.0 - - + -
249B ILE* 4.9 5.2 - - + -
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Residues in contact with ASN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PRO* 3.6 6.2 - - - +
97A ASP* 3.3 7.3 - - - +
202B PHE* 3.6 19.9 + - - -
203B TRP* 3.5 3.3 - - - +
204B MET* 2.9 49.7 + - + +
215B PRO* 5.4 0.7 - - - -
216B VAL* 1.3 78.0 - - - +
218B ALA* 1.3 93.5 + - - +
220B GLU* 3.2 18.8 + - - +
232B LYS* 3.0 30.3 + - - -
234B ARG* 3.6 12.1 + - - +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PRO* 4.2 7.9 - - - -
91A LYS* 3.7 27.4 - - + +
93A VAL* 4.0 21.1 - - + -
97A ASP* 2.6 29.6 + - + +
202B PHE 3.4 2.4 - - - +
215B PRO* 5.7 2.1 - - - +
217B ASN* 1.3 99.8 + - - +
219B ARG* 1.3 66.9 + - - +
220B GLU* 3.2 3.3 + - - +
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Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.7 27.5 - - - -
89A PRO* 3.0 25.0 + - + +
90A ALA* 3.0 24.0 + - - +
91A LYS 3.3 9.6 + - - +
92A ALA* 3.6 15.5 - - + +
93A VAL 3.1 25.8 + - - +
118A PHE* 4.2 4.0 - - - +
119A TRP* 2.6 36.1 + - - +
121A PRO* 3.5 23.4 - - - +
124A MET* 5.2 2.0 - - - +
201B GLU* 3.8 24.1 + - - +
202B PHE 3.5 4.3 - - - -
203B TRP* 3.6 31.1 - - + -
218B ALA* 1.3 71.7 - - - +
220B GLU* 1.3 59.9 + - - +
221B LYS* 4.3 1.3 + - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 4.0 12.1 - - + -
95A GLY 3.8 14.6 - - - +
96A VAL* 4.1 0.2 - - - -
97A ASP 2.8 26.1 + - - -
200B VAL 3.9 0.5 - - - +
201B GLU* 3.2 4.2 - - - -
202B PHE* 2.8 47.8 + - + +
217B ASN* 3.2 12.2 + - - +
218B ALA 3.7 10.1 - - - +
219B ARG* 1.3 74.3 - - - +
221B LYS* 1.3 62.8 + - - +
222B TRP* 2.7 32.7 + - + +
230B TYR* 2.5 25.2 + - - -
232B LYS* 3.2 15.6 + - - -
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL 4.6 4.2 + - - +
94A VAL* 4.7 9.2 + - - +
121A PRO* 6.1 0.8 - - - +
123A TYR* 3.8 20.4 + - - +
200B VAL 3.5 4.5 - - - -
201B GLU* 4.0 15.3 + - - +
219B ARG 4.3 1.5 + - - +
220B GLU* 1.3 74.6 - - - +
222B TRP* 1.3 75.4 + - - +
256B ILE* 3.8 26.9 - - + -
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Residues in contact with TRP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL 5.1 3.6 - - - -
95A GLY* 4.0 12.3 - - - -
96A VAL* 3.9 20.4 - - + -
190B LEU* 5.9 0.9 - - + -
198B ALA 3.5 1.7 - - - +
199B ASN* 3.4 4.7 - - - +
200B VAL* 2.8 51.1 + - + +
202B PHE* 5.2 6.7 - - + -
220B GLU* 2.7 40.0 + - + +
221B LYS* 1.3 86.8 - - - +
223B VAL* 1.3 72.8 + - - +
224B ILE* 3.8 13.2 - - + -
230B TYR* 3.6 41.6 - + + -
256B ILE* 5.2 0.7 - - - +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLU* 3.6 39.3 - - + +
198B ALA 3.6 3.1 - - - +
199B ASN* 3.3 19.3 - - - +
222B TRP* 1.3 84.0 - - - +
224B ILE* 1.3 65.5 + - - +
225B ALA* 4.0 2.6 + - - +
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B LEU* 4.4 10.5 - - + -
190B LEU* 4.2 17.9 - - + +
192B ASN* 2.8 32.8 + - + +
197B GLU* 3.4 2.4 - - - -
198B ALA* 2.9 29.5 + - + +
200B VAL* 4.1 20.9 - - + -
222B TRP* 4.2 13.5 - - + -
223B VAL* 1.3 75.1 - - - +
225B ALA* 1.3 66.0 + - - +
228B ASP* 3.6 32.1 - - + +
229B THR 4.4 1.6 - - - +
230B TYR* 4.1 27.8 - - + +
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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