Contacts of the strand formed by residues 259 - 266 (chain A) in PDB entry 3M2K
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 VAL 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 4.4 5.4 - - + -
49A LEU 2.9 22.0 - - - +
50A ASP* 3.5 33.7 - - + +
249A ILE* 3.5 5.5 - - - +
250A ILE* 3.0 41.6 + - + +
252A PRO* 4.8 5.9 - - + +
257A ASP 3.7 3.1 + - - +
258A PRO* 1.3 73.2 - - - +
260A VAL* 1.3 81.0 + - - +
261A LEU* 4.7 5.2 - - + -
286A VAL* 5.9 0.7 - - + -
287A MET* 5.6 8.7 - - + -
290A LEU* 3.6 23.8 - - + -
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Residues in contact with VAL 260 (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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48A ALA* 3.4 1.2 - - - -
49A LEU* 2.8 37.0 + - + +
51A THR* 4.1 11.7 - - + -
187A VAL* 3.5 41.6 - - + +
190A LEU* 4.5 12.8 - - + -
191A ARG* 3.9 22.0 - - + +
195A LEU* 3.7 24.5 - - + -
248A ALA 3.5 10.5 - - - +
249A ILE* 4.4 8.7 - - + -
259A VAL* 1.3 79.3 - - - +
261A LEU* 1.4 61.7 - - - +
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Residues in contact with LEU 261 (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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46A ILE* 4.6 0.4 - - + -
47A PHE 3.3 13.5 - - - +
48A ALA* 3.9 15.7 - - + -
187A VAL* 4.1 3.4 - - - -
190A LEU* 5.4 0.2 - - - +
221A ILE* 4.3 17.7 - - + -
246A ASP 3.9 0.5 - - - +
247A ILE* 3.3 3.2 - - - +
248A ALA* 2.7 43.7 + - - +
250A ILE* 3.6 30.3 - - + -
259A VAL* 4.7 2.2 - - + -
260A VAL* 1.4 78.2 - - - +
262A ALA* 1.3 79.7 + - - +
263A VAL* 4.1 15.9 - - + -
283A THR* 4.4 10.5 - - + +
286A VAL* 4.0 24.0 - - + -
287A MET* 5.6 1.1 - - - -
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Residues in contact with ALA 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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45A GLY 3.6 1.0 - - - +
46A ILE* 3.5 7.4 - - - -
47A PHE 2.9 27.5 + - - +
183A ALA* 3.9 20.3 - - - +
186A LEU* 4.7 1.3 - - + -
187A VAL* 3.6 20.8 - - + +
247A ILE* 3.3 25.8 - - + -
261A LEU* 1.3 76.6 - - - +
263A VAL* 1.3 61.2 - - - +
264A LEU* 4.2 3.8 - - + -
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Residues in contact with VAL 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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44A LEU* 4.9 4.7 - - + -
45A GLY 3.4 2.2 - - - -
46A ILE* 4.2 13.9 - - + -
221A ILE* 4.4 4.9 - - + -
244A ARG 4.2 0.3 - - - +
245A ASN* 3.4 3.3 - - - -
246A ASP 3.0 32.2 + - - +
261A LEU* 4.1 19.5 - - + -
262A ALA* 1.3 76.0 - - - +
264A LEU* 1.3 69.0 + - - +
279A ILE* 3.6 33.4 - - + +
282A ALA* 4.0 24.7 - - + -
283A THR* 4.1 20.9 - - - +
286A VAL* 5.4 0.7 - - + -
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Residues in contact with LEU 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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44A LEU* 3.1 6.9 - - - +
45A GLY 2.5 42.3 + - - +
66A PHE* 3.9 35.9 - - + +
68A PHE* 5.7 2.9 - - - -
71A THR* 5.1 2.2 - - + +
181A SER 5.1 1.1 - - - +
182A THR* 4.1 6.1 - - - -
183A ALA* 3.6 34.1 - - + +
186A LEU* 4.2 21.5 - - + -
244A ARG 3.9 0.7 - - - -
245A ASN* 3.1 35.0 - - + +
247A ILE* 4.6 12.3 - - + -
262A ALA* 4.9 0.7 - - + -
263A VAL* 1.3 84.6 - - - +
265A SER* 1.3 66.8 + - - +
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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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42A ALA* 4.9 1.6 - - - -
43A LYS 2.9 15.3 - - - -
44A LEU* 4.2 3.8 - - - -
66A PHE* 3.9 6.0 - - - -
242A GLY 4.1 1.4 + - - -
243A THR* 3.0 7.8 - - - +
244A ARG* 2.6 53.9 + - - +
245A ASN* 3.2 6.3 + - - -
264A LEU* 1.3 79.5 - - - +
266A SER* 1.3 60.7 + - - +
278A LEU* 3.9 22.6 - - - +
279A ILE* 3.6 10.0 - - - +
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Residues in contact with SER 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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42A ALA* 3.2 3.0 - - - +
43A LYS* 2.9 40.4 + - - +
66A PHE* 3.7 18.9 - - - -
241A TYR* 3.4 11.4 - - - -
242A GLY 3.4 9.4 - - - -
243A THR* 3.8 16.4 - - - -
265A SER* 1.3 77.0 - - - +
267A ARG* 1.3 70.6 + - - +
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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