Contacts of the strand formed by residues 251 - 258 (chain B) in PDB entry 4LOE
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 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ALA* 4.2 10.5 - - + -
162B ILE 3.3 11.4 - - - +
163B TYR* 3.5 30.1 - - + -
164B LYS* 4.1 1.6 - - - +
173B VAL* 4.1 8.3 - - + -
194B LEU* 3.6 29.6 - - + -
236B TYR* 4.8 4.0 - - + -
240B SER* 5.6 0.4 - - - +
246B MET* 3.7 23.1 - - + -
249B ARG 3.6 1.5 + - - +
250B PRO* 1.3 77.9 - - - +
252B LEU* 1.3 65.1 + - - +
253B THR* 5.0 0.4 - - - +
271B GLU* 3.2 11.0 - - - +
272B VAL* 3.1 56.0 + - + +
274B VAL* 5.6 1.1 - - + -
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Residues in contact with LEU 252 (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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100B GLN* 3.3 41.7 - - + +
131B ASN* 6.2 0.2 - - - +
161B ALA* 3.1 7.0 - - - +
162B ILE* 2.9 47.4 + - + +
164B LYS* 4.2 30.0 - - + +
251B ILE* 1.3 77.3 - - - +
253B THR* 1.3 64.4 + - - +
254B ILE* 4.0 2.6 + - + -
269B SER* 4.7 9.2 - - - +
270B PHE* 3.5 5.4 - - - +
271B GLU* 3.7 31.0 - - + +
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA* 4.5 3.1 - - + -
160B MET 3.4 7.4 - - - +
161B ALA* 4.4 2.5 - - - +
195B ILE* 4.0 14.2 - - + +
234B TYR* 6.0 1.3 - - + -
236B TYR* 2.6 39.6 + - - +
251B ILE* 4.5 0.7 + - - +
252B LEU* 1.3 72.9 + - - +
254B ILE* 1.3 63.4 + - - +
255B ILE* 3.8 19.4 + - + -
269B SER* 3.2 6.4 - - - -
270B PHE* 2.9 52.8 + - + -
272B VAL* 3.5 6.3 - - - +
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Residues in contact with ILE 254 (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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98B PRO* 4.4 10.1 - - + -
99B SER 3.8 17.5 - - - +
100B GLN* 4.1 9.4 - - + -
158B ARG 3.5 1.7 - - - +
159B ALA* 3.3 4.9 - - - -
160B MET* 2.7 43.6 + - + +
162B ILE* 4.1 39.7 - - + -
252B LEU* 4.8 3.4 - - + -
253B THR* 1.3 74.8 - - - +
255B ILE* 1.3 62.5 + - - +
256B THR* 4.0 11.1 + - + -
267B ARG* 3.9 31.0 - - + -
268B ASN 3.6 3.8 - - - +
269B SER* 4.2 11.0 - - - -
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.9 18.8 - - + -
111B LEU* 3.9 33.0 - - + -
143B VAL* 4.8 2.5 - - + -
145B LEU* 4.3 4.3 - - + -
157B VAL* 3.8 27.4 - - + -
158B ARG 3.2 1.8 - - - +
159B ALA* 3.7 27.4 - - + -
234B TYR* 3.8 17.9 - - + +
253B THR* 3.8 14.4 - - + -
254B ILE* 1.3 71.9 - - - +
256B THR* 1.3 63.2 + - - +
267B ARG* 3.4 3.8 - - - +
268B ASN 2.8 40.3 + - - +
270B PHE* 4.0 10.3 - - + -
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Residues in contact with THR 256 (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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109B PHE* 4.9 0.7 - - - -
156B ARG 3.7 0.3 - - - +
157B VAL* 3.5 5.5 - - - +
158B ARG* 2.8 54.3 + - - +
254B ILE* 4.0 10.1 + - + -
255B ILE* 1.3 77.0 - - - +
257B LEU* 1.3 61.6 + - - +
258B GLU* 4.0 8.7 + - - +
264B LEU* 4.1 12.6 - - + -
266B GLY 3.4 6.3 - - - +
267B ARG* 3.7 35.0 - - + +
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Residues in contact with LEU 257 (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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107B TYR* 4.9 7.4 - - + -
109B PHE* 4.1 43.6 - - + -
145B LEU* 5.1 0.2 - - + -
147B VAL* 4.8 2.7 - - + -
151B PRO* 4.1 22.2 - - + -
155B THR* 3.8 17.7 - - + -
156B ARG 3.5 2.5 - - - +
157B VAL* 3.9 26.5 - - + -
220B TYR* 4.4 10.5 - - + -
255B ILE 4.4 0.2 + - - -
256B THR* 1.3 72.7 - - - +
258B GLU* 1.3 60.6 + - - +
264B LEU* 3.8 3.8 - - - +
265B LEU* 2.7 36.2 + - + -
266B GLY* 2.9 22.8 + - - +
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Residues in contact with GLU 258 (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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155B THR* 3.5 4.7 - - - +
156B ARG* 2.7 58.3 + - + +
158B ARG* 2.9 51.0 + - + +
217B VAL* 5.0 0.2 - - - -
256B THR* 4.2 9.8 + - - +
257B LEU* 1.3 76.0 - - - +
259B ASP* 1.3 63.4 + - - +
262B GLY* 3.9 27.4 - - - +
263B ASN 3.1 13.9 - - - +
264B LEU* 4.8 1.8 - - + -
265B LEU* 3.5 6.5 - - - -
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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