Contacts of the strand formed by residues 264 - 274 (chain B) in PDB entry 4IBU
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 LEU 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B TYR* 3.7 31.7 + - + -
256B THR* 4.2 12.3 - - + -
257B LEU 3.9 4.3 - - - +
258B GLU* 4.7 3.4 - - + -
262B GLY 3.7 2.4 + - - -
263B ASN* 1.3 73.3 - - - +
265B LEU* 1.3 64.7 + - - +
266B GLY 3.3 29.4 - - - +
267B ARG* 3.3 37.5 - - + +
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Residues in contact with LEU 265 (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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103B TYR* 3.6 6.7 + - - -
104B GLN 4.0 1.2 - - - +
105B GLY* 3.4 23.9 - - - -
106B SER* 4.3 3.4 + - - +
107B TYR* 4.2 29.7 - - + +
152B PRO* 5.6 1.3 - - + -
155B THR* 4.0 20.0 - - + +
257B LEU* 2.7 27.3 + - + +
258B GLU 3.6 8.5 - - - +
259B ASP* 3.6 42.0 - - + +
263B ASN* 4.3 3.8 - - + +
264B LEU* 1.3 81.5 - - - +
266B GLY* 1.3 56.2 + - - +
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Residues in contact with GLY 266 (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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103B TYR* 3.1 17.3 - - - -
104B GLN 4.4 2.9 - - - -
109B PHE* 3.7 17.3 - - - -
256B THR* 3.4 1.2 - - - -
257B LEU* 2.8 27.1 + - - +
264B LEU* 3.3 14.0 - - - +
265B LEU* 1.3 80.2 - - - +
267B ARG* 1.3 61.3 + - - -
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Residues in contact with ARG 267 (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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99B SER* 3.3 50.9 + - - -
100B GLN 3.9 2.7 - - - -
101B LYS* 2.8 43.0 + - - +
102B THR* 3.6 3.8 - - - +
103B TYR* 2.7 43.2 + - + +
109B PHE* 3.7 8.1 - - - +
254B ILE* 3.8 12.5 - - + +
255B ILE 3.4 4.3 - - - -
256B THR* 3.8 21.8 - - + +
264B LEU* 3.3 32.7 - - + +
266B GLY* 1.3 76.2 - - - +
268B ASN* 1.3 70.0 + - - +
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Residues in contact with ASN 268 (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 5.4 0.2 - - - -
102B THR* 4.0 30.9 + - - +
109B PHE* 4.2 6.0 + - + -
110B ARG* 4.1 12.1 - - - +
111B LEU* 3.6 45.9 - - + +
131B ASN* 5.1 1.4 + - - -
254B ILE* 3.6 3.1 - - - +
255B ILE* 2.8 31.8 + - - +
267B ARG* 1.3 76.7 + - - +
269B SER* 1.3 85.2 + - - +
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Residues in contact with SER 269 (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* 3.5 29.5 + - - +
102B THR* 5.1 2.2 + - - -
111B LEU* 4.8 1.0 - - - +
131B ASN* 3.0 19.3 + - - +
252B LEU* 5.1 7.4 - - - +
253B THR 3.1 15.3 - - - -
254B ILE* 4.0 16.2 - - - -
268B ASN* 1.3 89.4 + - - +
270B PHE* 1.3 69.3 + - - +
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Residues in contact with PHE 270 (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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111B LEU* 3.8 10.1 - - + -
113B PHE* 3.7 25.8 - + + -
126B TYR* 4.6 1.1 - - + -
131B ASN* 3.6 25.8 - - - +
133B MET* 3.9 23.8 - - + -
143B VAL* 4.1 19.7 - - + -
234B TYR* 5.4 1.1 - + - -
236B TYR* 3.4 26.2 - - - -
252B LEU* 3.4 5.6 - - - -
253B THR* 2.7 45.9 + - + -
255B ILE* 3.9 24.7 - - + -
269B SER* 1.3 78.9 - - - +
271B GLU* 1.3 71.2 + - - +
272B VAL* 3.6 9.2 - - + -
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Residues in contact with GLU 271 (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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130B LEU* 4.6 7.0 - - - +
131B ASN* 2.9 17.0 + - - +
132B LYS* 2.8 43.9 + - + +
133B MET 2.7 27.7 + - - -
164B LYS* 2.9 35.8 + - + +
250B PRO* 3.6 16.9 - - + +
251B ILE 3.4 15.7 - - - +
252B LEU* 3.8 12.1 - - + +
270B PHE* 1.3 77.5 - - - +
272B VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 272 (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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132B LYS* 4.2 6.6 + - - -
133B MET* 3.2 12.6 - - + +
135B CYS* 4.2 7.9 - - - -
236B TYR* 3.6 23.6 - - + +
240B SER* 4.2 2.9 + - - -
250B PRO* 4.8 2.6 - - - +
251B ILE* 3.0 38.7 + - + +
253B THR* 3.3 28.3 - - - +
270B PHE* 3.6 14.6 - - + +
271B GLU* 1.3 81.7 - - - +
273B CYS* 1.3 65.6 + - - +
274B VAL* 4.0 24.0 - - + -
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Residues in contact with CYS 273 (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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132B LYS* 3.6 22.3 - - - +
133B MET 2.8 9.1 + - - +
134B PHE* 3.3 18.3 - - + -
135B CYS* 2.9 25.3 + - - +
240B SER* 3.4 17.5 - - - +
272B VAL* 1.3 75.0 - - - +
274B VAL* 1.3 64.1 + - - +
275B CYS* 3.8 27.2 + - - -
281B ASP* 4.8 4.0 - - - -
285B GLU* 4.9 5.4 - - - -
7E T 5.9 2.7 - - - -
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Residues in contact with VAL 274 (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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135B CYS* 3.1 14.6 - - - +
136B GLN 4.0 1.8 - - - -
137B LEU* 3.7 21.1 - - - +
236B TYR* 3.5 30.7 - - + -
238B CYS 3.4 24.9 - - - +
239B ASN* 3.6 16.5 - - - +
240B SER* 2.8 39.5 + - - +
241B SER 4.5 0.7 + - - -
246B MET* 4.6 7.4 - - + -
251B ILE* 5.5 0.9 - - + -
272B VAL* 4.0 14.8 - - + -
273B CYS* 1.3 72.1 - - - +
275B CYS* 1.3 63.0 + - - +
8E G 4.7 0.7 + - - -
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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