Contacts of the strand formed by residues 213 - 224 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77G TRP* 3.2 8.5 + - - -
79G SER* 2.6 46.1 + - - -
80G ILE 4.6 6.7 - - - +
81G LYS* 3.9 23.8 - - + -
87G TYR* 3.9 35.9 - - + -
88G PHE 5.3 0.2 - - - +
132G SER* 5.4 4.9 - - - -
134G GLN* 2.9 15.9 + - - +
1272G O4B 4.8 7.9 - - - +
205H THR* 3.9 29.4 - - + +
206H ALA 3.7 2.5 - - - -
207H VAL* 4.5 5.8 - - + +
211H GLY 3.5 9.1 + - - +
212H LEU* 1.3 76.5 - - - +
214H ILE* 1.3 58.4 + - - +
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Residues in contact with ILE 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G TRP* 3.5 33.4 - - + +
101G GLN* 4.9 2.0 - - + +
205H THR* 3.2 3.4 - - - -
206H ALA* 2.7 50.6 + - + +
212H LEU* 4.3 15.7 - - + -
213H ILE* 1.3 71.9 - - - +
215H PRO* 1.3 82.4 - - + +
216H VAL* 3.6 1.0 - - - +
236H ILE* 4.7 11.0 - - + -
242H TYR* 3.9 33.9 - - + +
247H TYR* 3.7 31.4 - - + -
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Residues in contact with PRO 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G TRP* 3.4 33.9 - - + -
78G LEU 4.5 3.8 - - - +
79G SER* 3.7 11.4 - - - +
89G PRO* 3.8 27.6 - - + -
91G LYS* 6.2 2.2 - - + -
101G GLN* 3.9 16.3 - - - +
204H MET 4.0 4.7 - - - +
205H THR* 4.6 1.8 - - + -
213H ILE 3.4 9.0 - - - +
214H ILE* 1.3 94.4 - - + +
216H VAL* 1.3 60.8 + - - +
217H ASN 5.1 1.8 - - - +
218H ALA* 5.6 1.6 - - - +
236H ILE* 5.6 0.5 - - - +
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Residues in contact with VAL 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G ASP* 4.6 0.2 - - - -
186H PHE* 5.6 0.9 - - + -
204H MET* 2.9 40.7 + - + +
205H THR 3.7 2.9 - - - +
206H ALA* 3.6 25.4 - - + +
214H ILE 3.6 13.5 - - - +
215H PRO* 1.3 75.4 - - - +
217H ASN* 1.3 58.7 - - - +
234H ARG* 2.9 39.3 + - + +
235H GLY 4.5 5.8 - - - +
236H ILE* 4.0 33.9 - - + -
249H ILE* 4.9 5.2 - - + -
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Residues in contact with ASN 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G PRO* 3.4 9.4 - - - +
97G ASP* 3.4 6.5 - - - +
202H PHE* 3.7 14.9 - - - -
203H TRP* 3.5 0.5 - - - +
204H MET* 2.9 48.6 + - + +
215H PRO 5.3 0.4 - - - -
216H VAL* 1.3 79.5 - - - +
218H ALA* 1.3 89.4 + - - +
220H GLU* 3.1 16.6 + - - +
232H LYS* 3.0 37.8 - - - +
234H ARG* 3.6 14.8 - - - +
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Residues in contact with ALA 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G PRO* 4.1 7.2 - - - -
91G LYS* 3.5 35.2 - - + +
93G VAL* 4.0 14.6 - - + +
97G ASP* 2.7 28.6 + - + +
202H PHE 3.4 3.5 - - - +
215H PRO* 5.6 2.5 - - - +
217H ASN* 1.3 91.7 + - - +
219H ARG* 1.3 65.7 + - - +
220H GLU* 3.2 5.0 + - - +
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Residues in contact with ARG 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G PHE* 3.4 33.6 - - - -
89G PRO* 2.8 26.8 + - + +
90G ALA* 2.9 24.9 + - - +
91G LYS 3.0 13.0 + - - +
92G ALA* 3.3 14.7 - - + +
93G VAL 2.9 29.1 + - - +
118G PHE* 4.0 5.5 - - - +
119G TRP* 2.4 37.5 + - - +
121G PRO* 3.5 20.4 - - - +
124G MET* 5.3 1.4 - - - +
201H GLU* 3.8 22.7 + - - +
202H PHE 3.5 4.7 - - - -
203H TRP* 3.6 31.6 - - + -
218H ALA* 1.3 69.6 - - - +
220H GLU* 1.3 59.5 - - - +
221H LYS* 4.3 1.0 + - - +
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Residues in contact with GLU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G VAL* 3.6 15.0 - - + -
95G GLY 3.5 19.6 - - - +
97G ASP 2.7 22.8 + - - -
200H VAL 3.9 0.3 - - - +
201H GLU* 3.2 4.7 - - - +
202H PHE* 2.8 46.2 + - + +
217H ASN* 3.1 16.7 - - - +
218H ALA 3.7 10.8 - - - +
219H ARG* 1.3 72.3 - - - +
221H LYS* 1.3 62.3 + - - +
222H TRP* 2.7 30.4 + - + +
230H TYR* 2.5 24.6 + - - -
232H LYS* 3.2 10.4 + - - -
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Residues in contact with LYS 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G VAL 4.1 7.1 + - - +
94G VAL* 4.0 12.7 + - - +
121G PRO* 5.6 2.8 - - - +
123G TYR* 3.5 27.4 + - - +
200H VAL 3.5 4.9 - - - -
201H GLU* 4.0 16.4 + - - +
219H ARG 5.6 1.3 - - - +
220H GLU* 1.3 73.6 - - - +
222H TRP* 1.3 76.4 + - - +
256H ILE* 3.8 20.2 - - + -
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Residues in contact with TRP 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G VAL 4.5 4.3 - - - -
95G GLY* 3.5 24.0 - - - -
96G VAL* 3.8 15.7 - - + -
190H LEU* 5.9 0.9 - - + -
198H ALA 3.5 1.7 - - - +
199H ASN* 3.5 5.3 - - - +
200H VAL* 2.8 50.7 + - + +
202H PHE* 5.2 6.5 - - + -
220H GLU* 2.7 37.0 + - + +
221H LYS* 1.3 86.6 - - - +
223H VAL* 1.3 74.1 + - - +
224H ILE* 4.2 13.5 - - + -
230H TYR* 3.6 41.3 - + - -
256H ILE* 5.2 0.9 - - - +
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Residues in contact with VAL 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H GLU* 3.5 38.4 - - + +
198H ALA 3.6 4.7 - - - +
199H ASN* 3.3 19.3 - - - +
222H TRP* 1.3 82.7 - - - +
224H ILE* 1.3 64.9 + - - +
225H ALA* 4.0 2.7 + - - +
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Residues in contact with ILE 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H LEU* 4.4 10.1 - - + -
190H LEU* 4.2 17.5 - - + +
192H ASN* 2.8 32.6 + - + +
197H GLU* 4.4 2.2 - - - -
198H ALA* 2.9 30.7 + - + +
200H VAL* 4.1 21.1 - - + -
222H TRP* 4.2 13.9 - - + -
223H VAL* 1.3 75.1 - - - +
225H ALA* 1.3 65.6 + - - +
228H ASP* 3.6 32.1 - - + +
229H THR* 4.4 3.4 - - - +
230H TYR* 4.1 26.7 - - + +
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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