Contacts of the strand formed by residues 213 - 224 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205G THR* 3.9 27.1 - - + +
206G ALA 3.7 2.2 - - - -
207G VAL* 4.5 3.8 - - + +
211G GLY 4.1 3.6 - - - +
212G LEU* 1.3 76.8 - - - +
214G ILE* 1.3 60.2 + - - +
77H TRP* 3.2 9.2 + - - -
79H SER* 2.7 48.1 + - - +
80H ILE 4.6 5.4 - - - +
81H LYS* 4.0 19.3 - - + -
87H TYR* 3.9 35.7 - - + -
88H PHE 5.3 0.2 - - - +
132H SER* 5.3 5.4 - - - -
134H GLN* 2.9 17.8 + - - +
1272H O4B 4.1 16.2 - - - +
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Residues in contact with ILE 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G THR* 3.2 3.6 - - - -
206G ALA* 2.7 49.2 + - + +
212G LEU* 4.3 15.0 - - + -
213G ILE* 1.3 73.3 - - - +
215G PRO* 1.3 81.2 - - + +
216G VAL* 3.3 0.9 + - - +
236G ILE* 4.7 10.5 - - + -
242G TYR* 3.9 40.4 - - + +
247G TYR* 3.8 31.2 - - + -
77H TRP* 3.6 26.5 - - + +
101H GLN* 4.9 2.9 - - + +
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Residues in contact with PRO 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G MET 4.0 4.9 - - - +
205G THR* 4.6 1.8 - - + -
213G ILE 3.4 9.2 - - - +
214G ILE* 1.3 93.7 - - + +
216G VAL* 1.3 60.4 + - - +
217G ASN 5.1 2.2 - - - +
218G ALA* 5.7 1.1 - - - +
236G ILE* 5.6 0.5 - - - +
77H TRP* 3.5 34.5 - - + -
78H LEU 4.7 2.2 - - - +
79H SER* 3.8 11.2 - - - +
89H PRO* 4.0 28.3 - - + -
91H LYS* 6.4 1.8 - - + -
101H GLN* 3.9 17.2 - - - +
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Residues in contact with VAL 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G PHE* 5.6 0.9 - - + -
204G MET* 2.9 40.2 + - + +
205G THR* 3.7 2.7 - - - +
206G ALA* 3.6 25.1 - - + +
214G ILE 3.3 13.4 + - - +
215G PRO* 1.3 75.5 - - - +
217G ASN* 1.3 59.0 - - - +
234G ARG* 2.9 38.6 + - + +
235G GLY 4.6 4.9 - - - +
236G ILE* 4.0 34.1 - - + -
249G ILE* 4.9 5.2 - - + -
97H ASP* 4.5 0.4 - - - -
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Residues in contact with ASN 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G PHE* 3.7 14.6 - - + -
203G TRP* 3.5 4.0 - - - +
204G MET* 2.9 49.2 + - + +
215G PRO* 5.4 0.7 - - - -
216G VAL* 1.3 77.8 - - - +
218G ALA* 1.3 90.3 + - - +
220G GLU* 3.1 16.7 + - - +
232G LYS* 3.0 37.8 - - - +
234G ARG* 3.6 15.4 - - - +
89H PRO* 3.6 5.8 - - - +
97H ASP* 3.3 7.0 + - - +
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Residues in contact with ALA 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G PHE 3.4 3.6 - - - +
203G TRP* 4.2 0.2 - - - -
215G PRO* 5.7 1.9 - - - +
217G ASN* 1.3 91.2 + - - +
219G ARG* 1.3 66.0 + - - +
220G GLU* 3.2 4.8 + - - +
89H PRO* 4.2 7.0 - - - -
91H LYS* 3.7 24.0 - - + +
93H VAL* 4.0 22.4 - - + -
97H ASP* 2.7 29.3 + - + +
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Residues in contact with ARG 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G GLU* 3.8 22.5 + - - +
202G PHE 3.5 3.8 - - - -
203G TRP* 3.6 31.9 - - + -
218G ALA* 1.3 71.5 - - - +
220G GLU* 1.3 59.9 + - - +
221G LYS* 4.3 1.0 + - - +
88H PHE* 3.6 27.7 - - - -
89H PRO* 3.0 24.4 + - + +
90H ALA* 2.9 24.9 + - - +
91H LYS 3.3 10.7 + - - +
92H ALA* 3.6 14.8 - - + +
93H VAL 3.1 25.8 + - - +
118H PHE* 4.2 3.4 - - - +
119H TRP* 2.7 36.3 + - - +
121H PRO* 3.5 23.4 - - - +
124H MET* 5.2 2.2 - - - +
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Residues in contact with GLU 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL 3.9 0.7 - - - +
201G GLU* 3.2 4.6 - - - -
202G PHE* 2.8 45.8 + - + +
217G ASN* 3.1 15.2 - - - +
218G ALA 3.7 10.1 - - - +
219G ARG* 1.3 74.5 - - - +
221G LYS* 1.3 63.4 + - - +
222G TRP* 2.7 33.2 + - + +
230G TYR* 2.5 25.0 + - - -
232G LYS* 3.2 11.5 + - - -
93H VAL* 4.0 12.3 - - + -
95H GLY 3.9 14.4 - - - +
96H VAL* 4.2 0.2 - - - -
97H ASP 2.8 26.8 + - - -
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Residues in contact with LYS 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL 3.5 4.7 - - - +
201G GLU* 4.0 15.5 + - - +
219G ARG 4.3 1.5 + - - +
220G GLU* 1.3 73.9 - - - +
222G TRP* 1.3 74.8 + - - +
256G ILE* 3.8 26.5 - - + -
93H VAL 4.6 4.8 + - - +
94H VAL 4.8 8.6 + - - +
95H GLY 5.7 0.2 - - - +
121H PRO* 6.1 1.0 - - - +
123H TYR* 3.9 19.7 + - - +
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Residues in contact with TRP 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G LEU* 5.9 0.9 - - + -
198G ALA 3.5 1.4 - - - +
199G ASN* 3.4 5.1 - - - +
200G VAL* 2.8 51.1 + - + +
202G PHE* 5.2 6.5 - - + -
220G GLU* 2.7 40.4 + - + +
221G LYS* 1.3 86.8 - - - +
223G VAL* 1.3 73.1 + - - +
224G ILE* 3.8 12.6 - - + -
230G TYR* 3.6 40.7 - + - -
256G ILE* 5.2 0.9 - - - +
94H VAL 5.1 4.3 - - - -
95H GLY* 4.0 12.1 - - - -
96H VAL* 3.9 20.6 - - + -
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Residues in contact with VAL 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G GLU* 3.6 38.1 - - + +
198G ALA 3.6 4.7 - - - +
199G ASN* 3.3 20.4 - - - +
222G TRP* 1.3 81.9 - - - +
224G ILE* 1.3 64.6 - - - +
225G ALA* 4.0 2.2 + - + +
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Residues in contact with ILE 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G LEU* 4.4 10.1 - - + -
190G LEU* 4.2 17.5 - - + +
192G ASN* 2.8 33.1 + - + +
197G GLU* 4.4 2.0 - - - -
198G ALA* 2.9 30.8 + - + +
200G VAL* 4.1 21.8 - - + -
222G TRP* 4.2 13.5 - - + -
223G VAL* 1.3 76.2 - - - +
225G ALA* 1.3 64.5 + - - +
228G ASP* 3.6 31.9 - - + +
229G THR 4.4 2.0 - - - +
230G 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