Contacts of the strand formed by residues 496 - 499 (chain A) in PDB entry 1MVM
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 GLN 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.6 20.1 - - + +
114A VAL 5.6 0.4 - - - -
115A ASP* 5.5 2.5 - - - +
179A ALA 3.7 1.0 - - - +
180A VAL* 3.3 2.3 - - - -
181A ASP* 2.6 50.6 + - + +
184A ASN* 4.7 2.8 + - - +
186A LEU* 4.7 2.0 + - - +
187A PRO 2.6 30.7 + - - -
188A TYR* 3.7 27.7 - - + +
189A THR* 3.5 28.5 + - - +
211A TYR* 4.3 8.6 + - - -
494A PRO 4.5 1.6 - - - +
495A GLY* 1.2 77.4 - - - -
497A MET* 1.3 60.5 + - - +
498A LEU* 3.9 8.0 - - + +
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Residues in contact with MET 497 (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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113A LEU* 3.8 1.6 - - - +
114A VAL* 2.9 52.0 + - + +
145A GLN* 3.7 44.6 - - + +
146A GLU* 5.1 1.1 - - - -
147A ILE* 2.5 51.1 - - + -
178A VAL* 4.8 2.7 - - + -
179A ALA 3.7 2.9 - - - +
180A VAL* 4.1 19.5 - - + +
265A PHE* 4.3 10.3 - - + -
267A THR* 5.1 2.0 - - - +
495A GLY 4.4 0.9 - - - +
496A GLN* 1.3 75.1 - - - +
498A LEU* 1.3 59.0 - - - +
499A VAL* 4.8 7.9 - - + -
525A PHE* 5.7 0.2 - - + -
527A TRP* 4.1 10.8 - - + -
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Residues in contact with LEU 498 (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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111A TRP* 4.3 11.2 - - + -
112A SER 3.6 3.6 - - - +
113A LEU* 3.8 32.5 - - + -
177A MET 4.1 0.3 - - - +
178A VAL* 3.5 3.8 - - - +
179A ALA* 2.7 49.7 + - + +
181A ASP* 4.9 0.9 - - + -
186A LEU* 4.0 12.3 - - + -
211A TYR* 3.9 23.1 - - + -
250A ILE* 3.3 31.0 - - + -
254A GLN* 3.7 21.8 - - - +
496A GLN* 4.6 8.5 - - + +
497A MET* 1.3 77.0 - - - +
499A VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 499 (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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73A LEU* 3.5 13.4 - - + +
111A TRP* 3.9 1.6 - - - -
112A SER* 2.5 49.5 + - - +
114A VAL* 3.6 26.5 - - + -
147A ILE* 4.8 7.9 - - + -
176A MET* 3.1 38.6 - - + -
177A MET 3.5 4.9 - - - +
178A VAL* 4.7 10.1 - - + -
208A ALA* 6.0 1.1 - - + -
497A MET* 4.8 5.2 - - + +
498A LEU* 1.3 78.7 - - - +
500A ARG* 1.3 63.8 + - - +
525A PHE* 3.6 12.8 - - + -
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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