Contacts of the strand formed by residues 998 - 1004 (chain A) in PDB entry 3MP1
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 998 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801A ALA* 4.8 4.3 - - - -
802A HIS* 3.8 2.2 - - - -
847A ALA 3.7 0.3 - - - +
848A VAL* 3.7 2.8 - - - -
849A GLU* 3.1 41.2 + - - +
893A TYR* 5.0 3.5 + - - -
996A PHE 4.0 1.6 + - - -
997A VAL* 1.3 78.5 - - - +
999A VAL* 1.3 65.1 + - - +
1000A LEU 4.0 0.7 - - - -
1068A MET* 3.6 20.6 - - - +
1B GLC 5.7 0.2 - - - -
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Residues in contact with VAL 999 (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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801A ALA* 4.3 0.9 - - - -
802A HIS* 3.0 32.0 + - + +
830A PHE* 6.4 0.4 - - + -
831A THR* 4.5 14.8 - - + +
834A ALA* 3.7 23.6 - - + -
845A PRO* 3.7 21.5 - - + -
846A ILE 4.3 1.6 - - - +
847A ALA 3.2 12.6 - - - +
848A VAL* 4.6 15.7 - - + -
997A VAL* 5.4 3.1 - - + -
998A GLY* 1.3 77.0 - - - +
1000A LEU* 1.3 78.0 + - - +
1001A SER* 2.8 18.4 + - - +
1067A ILE* 6.0 2.7 - - + -
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Residues in contact with LEU1000 (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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749A ILE* 5.4 5.2 - - + -
753A LYS* 4.1 33.4 - - + +
799A PHE* 4.3 19.5 - - + -
800A TRP* 3.8 26.0 - - - +
801A ALA* 4.4 4.0 - - - +
846A ILE* 2.8 41.5 + - + -
847A ALA* 2.9 20.8 + - + +
849A GLU* 4.6 16.9 + - - +
998A GLY 4.0 1.6 + - - -
999A VAL* 1.3 71.7 - - - +
1001A SER* 1.3 66.9 + - - +
1037A LEU* 4.2 26.7 - - + +
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Residues in contact with SER1001 (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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799A PHE* 3.2 10.3 - - - -
800A TRP 3.0 29.5 + - - -
802A HIS* 4.2 2.1 - - - +
805A PHE* 3.2 22.9 - - - -
835A VAL* 3.3 26.1 - - - +
843A ALA* 4.2 0.4 - - - -
844A TYR 3.3 12.8 - - - -
845A PRO* 3.8 0.9 - - - +
846A ILE* 4.0 1.8 - - - -
999A VAL* 2.8 21.8 + - - +
1000A LEU* 1.3 76.5 + - - +
1002A ALA* 1.3 60.7 + - - +
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Residues in contact with ALA1002 (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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797A ILE* 4.0 4.9 - - + -
798A ILE 3.3 4.9 - - - -
799A PHE* 3.5 30.5 - - + -
805A PHE* 3.8 2.2 - - - -
843A ALA* 3.3 2.9 - - - +
844A TYR* 2.9 43.4 + - + +
846A ILE* 4.3 2.8 - - + +
1001A SER* 1.3 72.3 - - - +
1003A GLY* 1.3 60.8 + - - +
1004A ILE 4.3 0.2 + - - -
1018A LEU* 3.8 26.0 - - + -
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Residues in contact with GLY1003 (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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797A ILE* 3.2 10.0 - - - +
798A ILE* 2.7 43.1 + - - -
805A PHE* 3.6 13.9 - - - -
814A LEU* 4.4 7.0 - - - -
842A ILE 4.5 2.9 - - - -
843A ALA* 4.1 5.8 - - - -
1002A ALA* 1.3 74.3 - - - +
1004A ILE* 1.3 63.4 + - - -
1005A ASN 4.1 0.2 - - - -
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Residues in contact with ILE1004 (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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796A ASP 3.6 8.5 - - - +
797A ILE* 4.8 0.7 - - + -
814A LEU* 3.4 6.8 - - - +
815A ALA* 2.9 39.3 + - + +
817A ILE* 5.0 10.3 - - + +
842A ILE 5.0 3.0 + - - -
844A TYR* 4.2 22.7 - - + -
1003A GLY* 1.3 77.3 - - - +
1005A ASN* 1.3 69.2 + - - +
1006A ALA 3.3 0.2 + - - -
1008A SER* 5.4 1.6 - - - -
1011A LYS* 3.9 36.1 - - + +
1014A ALA* 3.8 26.0 - - + -
1015A LYS* 4.2 9.9 - - + +
1018A LEU* 4.3 11.7 - - + -
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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