Contacts of the strand formed by residues 244 - 251 (chain A) in PDB entry 3V50
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 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A MET* 3.5 7.8 - - - +
216A VAL* 6.3 0.8 - - - +
235A THR* 4.1 10.3 + - - -
236A GLY* 2.8 43.6 + - - +
237A ALA* 3.8 12.1 - - - +
242A GLY 3.3 8.0 + - - +
243A ALA* 1.3 75.9 - - - +
245A GLY* 1.3 61.5 + - - +
264A TYR* 3.5 1.6 - - - -
265A LEU* 2.8 45.8 + - + +
272A MET* 3.1 39.4 - - - +
275A ARG* 4.3 11.0 - - + +
276A ASN* 2.8 25.6 + - - +
279A ILE* 3.7 19.1 - - + -
303A MA4 3.3 26.0 - - + +
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Residues in contact with GLY 245 (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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69A MET* 3.5 11.4 - - - +
71A THR* 4.3 3.8 - - - -
235A THR* 3.3 6.9 - - - +
236A GLY 2.9 32.5 + - - +
244A ARG* 1.3 80.7 + - - +
246A ILE* 1.3 63.0 + - - +
263A ILE 3.1 11.9 - - - -
264A TYR* 3.9 3.8 - - - -
279A ILE* 4.6 5.2 - - - -
303A MA4 4.8 1.6 - - - +
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Residues in contact with ILE 246 (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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71A THR* 4.3 2.1 - - - +
221A ILE* 3.8 29.4 - - + -
233A ASP* 4.0 9.0 - - + -
234A LYS 3.5 7.6 - - - +
235A THR* 3.8 17.9 - - + -
245A GLY* 1.3 76.1 - - - +
247A VAL* 1.3 77.1 + - - +
248A ALA* 4.1 10.5 - - + -
261A VAL 3.7 0.3 - - - +
262A VAL* 3.4 3.6 - - - +
263A ILE* 2.9 45.2 + - + +
264A TYR* 4.8 1.2 - - - -
279A ILE* 3.9 25.8 - - + -
302A MA4 4.2 22.4 - - + -
303A MA4 4.3 7.2 - - + -
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Residues in contact with VAL 247 (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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71A THR* 4.1 13.9 - - - +
74A VAL* 4.5 7.2 - - + -
186A MET* 3.7 20.6 - - + -
190A LEU* 3.5 22.7 - - + -
211A MET* 3.7 10.2 - - + +
233A ASP* 3.2 3.8 - - - +
234A LYS* 2.9 55.9 + - + +
246A ILE* 1.3 77.9 - - - +
248A ALA* 1.3 59.8 + - - +
261A VAL 3.7 3.8 - - - -
262A VAL* 4.0 8.1 - - + -
264A TYR* 3.7 23.3 - - - +
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Residues in contact with ALA 248 (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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190A LEU* 5.3 0.8 - - - +
211A MET* 4.6 1.6 - - - -
231A ILE* 4.0 7.6 - - + -
232A ALA 3.2 11.9 - - - +
246A ILE* 4.1 8.7 - - + -
247A VAL* 1.3 75.7 - - - +
249A LEU* 1.3 65.6 + - - +
260A ILE* 3.3 8.1 - - - +
261A VAL* 2.8 36.2 + - + +
262A VAL* 5.3 0.4 - - - +
302A MA4 3.4 35.9 - - + -
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Residues in contact with LEU 249 (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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51A LEU* 4.3 13.2 - - + -
190A LEU* 6.2 1.6 - - + -
194A LEU* 4.0 24.9 - - + -
208A LEU* 3.4 32.8 - - + -
211A MET* 4.6 10.8 - - + -
230A PHE* 3.6 14.4 - - + +
231A ILE* 3.4 10.2 - - - +
232A ALA* 2.8 38.7 + - + +
248A ALA* 1.3 75.2 - - - +
250A LEU* 1.3 61.7 + - - +
257A ALA* 4.1 14.4 - - + -
259A ARG 3.2 6.1 - - - +
260A ILE* 3.5 31.4 - - + -
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Residues in contact with LEU 250 (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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225A LEU* 4.3 23.8 - - + -
229A TRP* 3.9 20.4 - - + -
230A PHE* 3.3 18.4 - - - +
231A ILE* 4.4 2.5 - - + -
249A LEU* 1.3 75.6 - - - +
251A GLY* 1.3 62.4 + - - +
256A LYS 3.9 4.3 - - - -
257A ALA* 4.6 1.0 - - - +
258A GLU 3.3 1.2 + - - -
259A ARG 2.9 33.6 + - - +
261A VAL* 4.4 12.8 - - + -
283A GLY* 5.3 2.0 - - - +
286A LEU* 4.7 8.7 - - + -
287A ILE* 4.8 9.2 - - + -
290A TRP* 3.7 28.4 - - + -
302A MA4 4.1 33.0 - - + -
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Residues in contact with GLY 251 (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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229A TRP* 3.2 10.5 - - - -
230A PHE* 2.8 29.7 + - - +
250A LEU* 1.3 79.2 - - - +
252A PRO* 1.3 77.0 - - - +
256A LYS 3.2 14.5 + - - +
258A GLU* 4.2 2.5 - - - -
290A TRP* 3.8 7.2 - - - -
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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