Contacts of the strand formed by residues 261 - 270 (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 ARG 261 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G GLU* 4.9 7.8 + - - +
161G LEU* 3.9 1.5 - - - +
203G TRP* 4.5 3.1 - - - -
252G GLN* 3.2 31.5 + - + +
253G VAL 3.4 10.3 - - - +
254G VAL* 3.9 22.4 - - + -
259G GLY 3.4 5.8 + - - +
260G GLU* 1.3 75.9 - - - +
262G VAL* 1.3 72.8 + - - +
263G GLU* 3.2 27.1 + - - +
84H GLU* 2.8 44.7 + - - +
85H GLY 4.1 0.4 + - - -
86H ILE* 3.4 26.2 - - - +
124H MET* 5.6 2.0 - - - -
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Residues in contact with VAL 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G PRO* 3.7 27.1 - - + -
160G GLU 4.1 14.6 - - - +
161G LEU* 3.7 16.6 - - + -
166G ILE* 3.9 34.3 - - + -
252G GLN* 3.4 5.2 - - - +
253G VAL* 2.9 37.1 + - + +
261G ARG* 1.3 78.3 - - - +
263G GLU* 1.3 67.2 + - - +
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Residues in contact with GLU 263 (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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83G PRO* 5.8 2.7 - - + -
84G GLU* 4.1 14.0 + - - +
85G GLY 4.9 0.5 + - - -
159G PRO* 3.5 18.4 - - - +
166G ILE* 5.7 1.8 - - - -
250G ASN* 3.0 18.6 - - - +
251G ALA 3.3 5.6 - - - +
252G GLN* 3.5 23.9 - - + +
261G ARG* 3.2 23.4 + - - +
262G VAL* 1.3 84.3 - - - +
264G GLN* 1.3 64.8 + - - +
265G SER* 5.0 0.9 - - - +
1272G O4B 3.9 18.5 - - - +
84H GLU 3.9 6.4 - - - +
85H GLY* 3.6 11.5 - - - +
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Residues in contact with GLN 264 (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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158G LEU* 5.1 5.3 - - - +
159G PRO* 3.3 32.5 - - + +
166G ILE* 3.3 18.2 + - + +
167G ASP* 4.3 1.1 - - - +
168G ILE* 3.6 47.3 + - + +
169G LYS* 5.7 0.5 - - - +
249G ILE 4.0 0.2 - - - +
250G ASN* 3.6 0.5 - - - +
251G ALA* 2.8 35.8 + - - +
263G GLU* 1.3 74.9 - - - +
265G SER* 1.3 72.4 + - - +
266G MET* 4.0 5.5 - - + +
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Residues in contact with SER 265 (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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248G THR* 4.3 4.9 - - - -
249G ILE 3.2 7.9 - - - -
250G ASN* 2.8 26.0 + - - -
263G GLU* 4.2 2.3 + - - +
264G GLN* 1.3 78.9 - - - +
266G MET* 1.3 70.3 + - - +
1272G O4B 3.3 45.2 - - - +
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Residues in contact with MET 266 (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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168G ILE* 3.7 46.9 - - + +
169G LYS* 5.1 0.4 - - - -
170G ASN* 4.0 18.6 - - + +
186G PHE* 4.0 24.2 - - + -
204G MET* 5.2 0.4 - - + -
248G THR* 3.5 3.4 - - - -
249G ILE* 2.6 66.1 + - + +
251G ALA 5.1 1.3 - - - +
264G GLN* 4.0 7.4 - - + +
265G SER* 1.3 87.2 - - - +
267G THR* 1.3 63.3 + - - +
1272G O4B 6.2 0.2 - - - -
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Residues in contact with THR 267 (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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170G ASN* 5.1 1.6 + - - -
175G ASN* 4.2 17.4 + - - +
246G GLU* 4.1 22.9 + - - +
247G TYR 3.4 8.3 + - - -
248G THR* 4.8 5.8 - - - -
266G MET* 1.3 80.0 - - - +
268G VAL* 1.3 68.9 + - - +
269G VAL* 4.9 5.0 + - - +
1272G O4B 4.3 25.6 - - - -
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Residues in contact with VAL 268 (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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170G ASN* 4.2 3.1 - - - +
174G ILE 4.2 14.8 - - - +
175G ASN 3.7 8.5 - - - +
176G SER* 4.3 7.9 - - - -
177G VAL* 4.7 2.2 - - + +
184G VAL* 4.4 10.5 - - + -
186G PHE* 4.1 15.5 - - + -
238G PHE* 3.7 34.3 - - + -
247G TYR* 2.7 47.1 + - - +
249G ILE* 4.0 17.7 - - + -
266G MET* 4.1 0.6 + - + -
267G THR* 1.3 81.7 + - - +
269G VAL* 1.3 68.9 + - - +
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Residues in contact with VAL 269 (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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175G ASN 3.2 16.2 + - - +
176G SER* 3.1 14.1 - - - -
177G VAL 3.0 23.9 + - - -
245G GLY* 3.3 14.8 - - - +
246G GLU* 4.4 12.6 - - + +
267G THR* 4.9 7.6 - - - +
268G VAL* 1.3 77.2 - - - +
270G LYS* 1.3 72.1 + - - +
271G LYS* 4.2 14.1 - - + +
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Residues in contact with LYS 270 (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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177G VAL* 3.6 15.0 - - + -
178G GLU 4.0 13.2 - - - +
179G SER* 2.9 30.9 + - - +
181G GLY* 4.6 1.1 - - - -
238G PHE* 4.6 11.2 - - + -
239G ASP 3.3 21.5 - - - -
240G LYS* 3.0 8.3 + - - +
242G TYR* 2.6 37.4 + - + +
243G PRO 3.7 10.1 - - - +
244G ALA* 3.4 1.9 - - - +
245G GLY 2.7 35.4 + - - +
247G TYR* 3.8 21.4 - - + -
268G VAL* 4.1 1.4 + - - +
269G VAL* 1.3 74.7 - - - +
271G LYS* 1.3 71.1 + - - +
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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