Contacts of the strand formed by residues 261 - 270 (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 ARG 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU* 4.6 8.4 + - - +
161A LEU* 3.9 2.0 - - - +
203A TRP* 4.5 2.2 - - - -
252A GLN* 3.2 33.5 + - + +
253A VAL 3.4 10.3 - - - +
254A VAL* 3.9 22.4 - - + -
259A GLY 3.4 6.1 + - - +
260A GLU* 1.3 75.1 - - - +
262A VAL* 1.3 72.7 + - - +
263A GLU* 3.2 25.3 + - - +
84B GLU* 2.5 46.1 + - - +
85B GLY 3.9 1.8 + - - -
86B ILE* 3.4 23.9 - - - +
124B MET* 5.7 1.8 - - - -
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Residues in contact with VAL 262 (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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159A PRO* 3.7 26.2 - - + -
160A GLU 4.1 14.1 - - - +
161A LEU* 3.7 17.9 - - + -
166A ILE* 3.9 34.1 - - + -
252A GLN* 3.4 4.9 - - - +
253A VAL* 2.9 37.4 + - + +
261A ARG* 1.3 76.6 - - - +
263A GLU* 1.3 66.1 - - - +
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Residues in contact with GLU 263 (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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83A PRO* 5.8 2.9 - - - -
84A GLU 4.2 13.0 + - - -
85A GLY 4.8 0.5 + - - -
159A PRO* 3.5 19.1 - - - +
166A ILE* 5.7 1.8 - - - -
250A ASN* 3.0 17.6 - - - +
251A ALA 3.3 5.4 - - - +
252A GLN* 3.5 27.9 - - + +
261A ARG* 3.2 20.4 + - - +
262A VAL* 1.3 81.6 - - - +
264A GLN* 1.3 63.4 + - - +
265A SER* 5.0 0.7 - - - +
1272A O4B 3.8 18.9 - - - +
84B GLU 4.1 5.4 - - - +
85B GLY* 3.6 9.5 - - - +
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Residues in contact with GLN 264 (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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157A SER 5.5 1.6 + - - -
158A LEU* 5.0 4.2 - - - +
159A PRO* 3.7 21.8 - - + +
166A ILE* 3.6 17.5 - - + +
167A ASP* 4.2 2.3 - - - +
168A ILE* 3.4 53.7 + - + +
249A ILE 4.0 0.3 - - - +
250A ASN* 3.6 0.2 - - - -
251A ALA* 2.8 36.7 + - - +
263A GLU* 1.3 76.2 - - - +
265A SER* 1.3 72.8 + - - +
266A MET* 4.1 5.3 - - + +
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Residues in contact with SER 265 (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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248A THR* 4.3 5.8 - - - -
249A ILE 3.2 7.6 - - - -
250A ASN* 2.8 19.8 + - - -
263A GLU* 4.2 1.7 + - - +
264A GLN* 1.3 79.4 - - - +
266A MET* 1.3 69.7 + - - +
1272A O4B 2.7 47.1 - - - -
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Residues in contact with MET 266 (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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168A ILE* 3.7 44.9 - - + +
169A LYS* 4.2 0.7 - - - -
170A ASN* 4.0 17.0 - - + +
186A PHE* 4.0 27.1 - - + -
204A MET* 5.2 0.4 - - + -
248A THR* 3.5 3.8 - - - -
249A ILE* 2.6 66.3 + - + +
251A ALA 5.1 1.6 - - - +
264A GLN* 4.1 7.0 - - + +
265A SER* 1.3 86.3 - - - +
267A THR* 1.3 62.8 + - - +
268A VAL* 5.7 0.2 - - + -
1272A O4B 6.3 0.4 - - - -
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Residues in contact with THR 267 (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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170A ASN* 5.1 1.4 + - - -
175A ASN* 4.2 16.9 + - - +
246A GLU* 4.1 24.7 + - - +
247A TYR 3.4 9.0 + - - -
248A THR* 4.8 6.1 - - - -
266A MET* 1.3 78.6 - - - +
268A VAL* 1.3 68.9 + - - +
269A VAL* 4.9 5.1 + - - +
1272A O4B 4.7 18.8 - - - +
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Residues in contact with VAL 268 (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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170A ASN* 4.2 3.1 - - - +
174A ILE 4.2 13.9 - - - +
175A ASN 3.7 9.0 - - - +
176A SER* 4.3 8.5 - - - -
177A VAL* 4.7 1.8 - - + +
184A VAL* 4.4 11.7 - - + -
186A PHE* 4.1 15.5 - - + -
238A PHE* 3.7 33.7 - - + -
247A TYR* 2.7 47.1 + - - +
249A ILE* 4.0 18.4 - - + -
266A MET 5.3 0.2 - - - -
267A THR* 1.3 80.3 + - - +
269A VAL* 1.3 68.1 + - - +
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Residues in contact with VAL 269 (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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175A ASN* 3.2 16.2 + - + +
176A SER* 3.1 13.9 - - - -
177A VAL 3.0 23.4 + - - -
245A GLY* 3.3 16.2 - - - +
246A GLU* 4.5 11.2 - - + +
267A THR* 4.9 6.5 - - - +
268A VAL* 1.3 78.3 - - - +
270A LYS* 1.3 68.8 + - - +
271A LYS* 4.2 14.6 - - + +
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Residues in contact with LYS 270 (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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177A VAL* 3.6 13.7 - - + -
178A GLU 4.0 13.5 - - - +
179A SER* 2.9 31.5 + - - +
181A GLY* 4.6 0.4 - - - -
238A PHE* 4.6 11.9 - - + -
239A ASP 3.3 20.4 - - - -
240A LYS* 3.0 9.0 + - - +
242A TYR* 2.6 37.7 + - + +
243A PRO 3.7 10.5 - - - +
244A ALA* 3.3 2.1 - - - +
245A GLY* 2.7 35.8 + - - +
247A TYR* 3.8 20.9 - - + -
268A VAL* 4.1 1.4 + - - +
269A VAL* 1.3 73.8 - - - +
271A LYS* 1.3 70.2 + - - +
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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