Contacts of the strand formed by residues 243 - 251 (chain B) in PDB entry 2W77
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 TYR 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B ARG* 2.9 26.9 + - - -
177B MET* 3.8 2.6 - - + +
219B TYR* 3.6 23.8 - + + -
238B SER* 4.2 9.5 - - - -
239B ASP 3.5 23.8 - - - -
240B MET* 3.1 24.6 + - + +
242B ILE* 1.3 99.1 - - + +
244B ASP* 1.3 61.5 + - - +
245B ARG 4.4 8.1 - - - +
246B VAL* 5.4 0.2 - - + -
268B LEU* 3.4 43.1 - - + -
269B ILE 3.2 19.5 - - - +
270B ARG* 3.8 23.3 + - + -
271B LYS* 3.7 8.9 - - - -
351B ASP* 5.1 1.7 + - - -
353B GLN* 6.0 0.2 - - - -
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Residues in contact with ASP 244 (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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140B ILE* 3.4 15.7 - - + +
141B THR* 3.1 23.6 + - - -
142B GLU* 3.2 23.8 + - - +
174B ARG* 3.2 31.6 + - - +
177B MET* 4.9 1.8 - - - -
243B TYR* 1.3 73.2 - - - +
245B ARG* 1.3 97.0 + - - +
269B ILE* 2.8 15.0 + - + +
270B ARG 4.3 11.7 - - - +
271B LYS* 4.0 6.0 - - - +
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Residues in contact with ARG 245 (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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137B LEU* 3.1 21.0 + - - +
138B GLY 3.9 5.1 + - - -
139B THR 3.5 31.7 + - - -
140B ILE* 3.9 5.9 - - - +
141B THR* 3.7 17.4 + - - +
149B PRO* 5.7 2.0 - - - -
151B THR 4.7 1.5 + - - -
152B ILE* 4.5 7.3 - - - +
171B VAL* 4.0 21.3 - - + -
172B VAL 3.4 16.2 - - - +
177B MET* 4.5 4.7 - - - -
243B TYR* 3.7 3.0 - - - +
244B ASP* 1.3 98.0 + - - +
246B VAL* 1.3 65.6 + - - +
247B GLU* 2.7 34.9 + - + -
268B LEU* 3.9 0.7 - - - -
269B ILE* 3.1 56.5 + - + +
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Residues in contact with VAL 246 (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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171B VAL* 3.5 4.1 - - - +
172B VAL* 3.1 29.2 + - + +
177B MET* 4.6 2.7 - - - -
185B ILE* 4.0 14.4 - - + -
188B VAL* 4.0 18.8 - - + -
189B MET* 4.1 12.6 - - + -
240B MET* 3.9 27.6 - - - -
243B TYR* 5.4 1.1 - - + -
245B ARG* 1.3 77.8 - - - +
247B GLU* 1.3 62.9 + - - +
248B VAL* 3.8 5.5 + - + +
266B ILE* 3.8 29.2 - - + -
267B ASN 3.5 4.9 - - - +
268B LEU* 4.3 11.7 - - + -
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Residues in contact with GLU 247 (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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137B LEU 3.6 7.1 - - - +
152B ILE* 3.4 12.1 - - + +
153B ALA 4.7 0.2 + - - -
154B THR* 2.6 39.2 + - + +
169B ILE* 4.6 3.6 - - + -
170B THR 3.8 3.8 - - - -
171B VAL* 4.3 16.2 - - + -
245B ARG* 2.7 35.6 + - + +
246B VAL* 1.3 74.4 - - - +
248B VAL* 1.3 60.9 + - - +
249B LEU 4.0 0.5 + - - -
265B THR 3.8 1.0 - - - +
266B ILE* 3.7 1.7 - - - -
267B ASN* 2.6 71.9 + - + +
269B ILE* 3.9 5.3 - - + +
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Residues in contact with VAL 248 (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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169B ILE* 3.7 2.9 - - - -
170B THR* 2.7 45.0 + - - +
172B VAL* 6.2 0.9 - - + -
189B MET* 3.6 31.4 - - + -
192B THR* 4.3 12.6 - - + -
195B ILE* 3.8 21.3 - - + -
246B VAL* 4.3 7.0 - - + +
247B GLU* 1.3 75.9 - - - +
249B LEU* 1.3 61.4 + - - +
250B LYS* 3.8 20.6 + - + +
264B ALA* 4.3 8.7 - - + -
265B THR 3.6 7.2 - - - +
266B ILE* 4.1 11.0 - - + -
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Residues in contact with LEU 249 (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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154B THR* 3.8 27.6 - - + +
155B ALA* 4.1 20.9 - - + +
165B THR* 6.1 0.2 - - + -
167B GLN* 3.5 35.9 - - + +
168B SER 3.3 17.7 - - - +
169B ILE* 3.6 16.4 - - + -
247B GLU 4.0 0.8 + - - -
248B VAL* 1.3 71.6 - - - +
250B LYS* 1.3 63.1 + - - +
253B THR* 3.7 26.0 - - + +
256B LEU* 6.5 0.4 - - + -
264B ALA* 3.0 5.5 - - - -
265B THR* 2.9 42.1 + - + +
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Residues in contact with LYS 250 (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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167B GLN* 5.1 2.9 + - - +
168B SER* 3.1 30.2 + - - +
170B THR* 2.9 32.6 + - - +
193B PRO 3.2 20.3 + - - -
194B GLY* 4.3 6.5 - - - +
195B ILE* 4.8 3.1 - - + -
209B ALA* 4.9 12.3 - - + -
210B ARG* 3.2 30.6 + - + +
248B VAL* 4.0 21.3 - - + +
249B LEU* 1.3 82.0 - - - +
251B GLY* 1.3 57.9 + - - +
253B THR* 5.0 0.7 - - - -
263B GLY 3.6 7.4 - - - +
264B ALA* 4.3 1.1 - - + +
615B ASN* 5.3 0.3 + - - -
617B GLU* 4.4 1.7 - - - +
674B GLU* 2.8 34.4 + - - +
676B GLU* 3.0 11.9 + - - -
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Residues in contact with GLY 251 (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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167B GLN* 5.9 0.4 - - - -
210B ARG* 3.4 17.2 - - - +
249B LEU 4.0 1.0 + - - -
250B LYS* 1.3 74.1 - - - +
252B ALA* 1.3 60.4 + - - -
253B THR* 4.2 2.8 + - - +
262B LEU* 4.1 1.2 - - - +
263B GLY* 2.9 40.0 + - - -
264B ALA 3.9 0.5 + - - -
615B ASN* 3.5 16.2 - - - -
638B ILE* 4.4 5.7 - - - +
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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