Contacts of the strand formed by residues 240 - 247 (chain A) in PDB entry 1MMG
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 GLY 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A PHE* 1.3 77.0 - - - +
241A LYS* 1.4 64.2 + - - +
260A SER* 3.2 5.9 - - - -
261A TYR* 2.8 43.3 + - - -
262A LEU* 5.0 1.8 - - - +
454A ASP 3.6 8.1 - - - -
455A ILE* 3.7 16.4 - - - -
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Residues in contact with LYS 241 (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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186A THR* 4.1 14.1 + - - +
189A THR* 4.1 13.5 - - - -
219A ASN* 4.1 19.5 + - - +
222A LEU* 5.7 2.9 - - + -
223A GLU* 5.0 2.2 + - - +
237A SER* 4.5 6.7 + - - -
239A PHE* 4.1 28.7 + - + -
240A GLY* 1.4 78.5 - - - +
242A PHE* 1.3 62.5 + - - +
243A ILE* 3.9 22.9 - - + -
258A ILE* 4.5 9.2 - - + -
259A GLN 3.1 11.4 - - - +
261A TYR* 4.2 4.3 - - - -
452A VAL 5.0 0.2 - - - +
453A LEU* 3.4 7.3 - - - +
454A ASP* 2.4 75.7 + - + +
455A ILE* 3.7 2.4 - - - +
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Residues in contact with PHE 242 (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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174A SER* 5.1 0.9 - - - -
241A LYS* 1.3 74.4 - - - +
243A ILE* 1.3 63.0 + - - +
244A GLU* 4.8 16.1 - - + +
257A SER 3.8 1.0 - - - +
258A ILE* 3.5 2.8 - - - -
259A GLN* 2.7 43.7 + - + +
261A TYR* 3.9 20.0 - - + +
449A PHE* 4.7 4.7 - + - -
451A GLY* 3.8 35.7 - - - -
452A VAL 3.2 10.5 - - - -
453A LEU* 3.7 23.8 - - + -
641A LEU* 4.1 11.9 - - + -
644A THR* 4.3 21.5 - - + -
645A LEU* 4.0 29.2 - - + -
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Residues in contact with ILE 243 (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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189A THR* 4.9 4.5 - - + -
193A ILE* 4.1 20.0 - - + -
215A ILE* 6.3 0.7 - - + -
219A ASN* 3.9 24.7 - - - +
222A LEU* 6.4 0.2 - - + -
241A LYS* 3.9 26.9 - - + -
242A PHE* 1.3 74.4 - - - +
244A GLU* 1.3 66.0 + - - +
245A ILE* 3.7 25.2 + - + +
256A ALA* 5.0 3.6 - - + -
257A SER 3.5 7.0 - - - +
258A ILE* 4.2 20.4 - - + -
450A ILE 3.6 1.2 - - - +
451A GLY* 2.9 4.9 - - - -
452A VAL* 2.6 49.8 + - + +
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Residues in contact with GLU 244 (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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242A PHE* 4.0 14.3 + - + -
243A ILE* 1.3 74.6 - - - +
245A ILE* 1.3 58.1 + - - +
246A GLN* 2.7 33.5 + - + +
256A ALA* 3.0 10.7 - - - +
257A SER* 2.6 44.8 + - - +
446A LYS* 3.4 12.1 + - - -
449A PHE* 3.5 46.1 - - + -
450A ILE 3.9 1.3 - - - -
451A GLY* 4.2 1.3 - - - -
644A THR* 5.4 2.8 - - - +
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Residues in contact with ILE 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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193A ILE* 3.8 35.9 - - + -
196A LEU* 3.8 19.5 - - + -
215A ILE* 4.6 9.2 - - + -
243A ILE* 3.8 15.3 - - + +
244A GLU* 1.3 71.9 - - - +
246A GLN* 1.4 65.0 + - - +
247A PHE* 3.1 29.5 - - + -
253A ILE* 4.2 20.2 - - + -
255A GLY 4.1 5.2 - - - +
256A ALA* 4.4 8.5 - - + -
449A PHE* 3.1 4.3 - - - -
450A ILE 2.8 47.1 + - - +
452A VAL* 5.1 3.1 - - + -
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Residues in contact with GLN 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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244A GLU* 2.7 31.3 + - + +
245A ILE* 1.4 72.8 - - - +
247A PHE* 1.3 56.4 + - - +
253A ILE* 3.3 8.0 - - - +
254A SER* 2.6 32.7 + - - +
255A GLY 3.0 19.9 + - - +
256A ALA* 3.4 15.7 + - - +
257A SER* 3.8 7.3 + - - -
442A CYS* 3.4 21.6 - - - -
443A SER* 2.8 42.7 + - - +
446A LYS* 3.6 25.5 - - + +
448A TYR 3.5 4.0 - - - -
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Residues in contact with PHE 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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163A TYR* 3.8 6.3 - + - -
166A MET* 3.6 29.4 - - + -
196A LEU* 4.0 19.1 - - + -
200A ALA* 3.8 14.6 - - + -
245A ILE* 3.1 41.7 - - + -
246A GLN* 1.3 72.1 - - - +
248A ASN* 1.3 65.9 + - - +
251A GLY 3.8 18.2 - - - -
252A PHE 3.0 13.7 - - - +
253A ILE* 3.7 19.5 - - + -
254A SER* 2.9 8.3 + - - -
447A ALA 3.3 7.4 + - - -
448A TYR* 3.0 31.1 + - + +
449A PHE* 4.1 2.9 - - - -
450A ILE* 3.7 25.1 - - + -
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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