Contacts of the strand formed by residues 1033 - 1038 (chain D) in PDB entry 5MS0
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 GLY1033 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032D SER* 1.3 79.5 - - - +
1034D PHE* 1.3 60.3 + - - +
1080D ILE* 6.2 0.4 - - - -
1081D VAL 3.5 9.0 - - - -
1082D ASP* 4.6 7.6 - - - -
1083D ALA 5.7 0.2 - - - -
1114D GLN* 3.4 10.6 - - - +
1115D ILE* 3.3 28.0 + - - +
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Residues in contact with PHE1034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033D GLY* 1.3 75.5 - - - +
1035D VAL* 1.3 62.0 + - - +
1036D ARG* 3.9 0.4 + - - -
1080D ILE* 3.4 8.8 - - - +
1081D VAL* 2.7 40.9 + - + +
1082D ASP 4.6 9.6 - - - +
1083D ALA* 6.1 0.2 - - - -
1112D GLY* 4.6 13.5 - - - +
1113D VAL 3.9 9.6 - - - +
1114D GLN* 5.2 0.9 - - - -
1115D ILE* 5.0 2.5 - - - +
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Residues in contact with VAL1035 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034D PHE* 1.3 74.5 - - - +
1036D ARG* 1.3 60.1 + - - +
1037D PHE 4.3 0.5 + - - -
1078D LEU* 5.3 12.3 - - + -
1079D LYS 4.0 3.1 - - - -
1080D ILE* 5.0 1.1 - - - +
1109D LEU* 6.1 3.6 - - + -
1110D GLU 4.7 12.1 - - - +
1111D ASP* 4.2 2.1 - - - -
1112D GLY* 3.1 26.6 + - - +
1113D VAL 3.8 13.3 + - - +
1115D ILE* 5.8 6.0 - - + +
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Residues in contact with ARG1036 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034D PHE 5.2 1.1 - - - +
1035D VAL* 1.3 72.5 - - - +
1037D PHE* 1.3 65.7 + - - +
1038D THR 3.4 0.7 + - - -
1077D ALA 3.8 1.7 - - - +
1078D LEU* 3.9 2.9 - - - -
1079D LYS* 3.0 44.7 + - + +
1081D VAL* 5.2 9.4 - - + -
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Residues in contact with PHE1037 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035D VAL 4.2 1.0 + - - -
1036D ARG* 1.3 73.6 - - - +
1038D THR* 1.3 58.2 + - - +
1040D MET* 5.2 12.6 - - + +
1077D ALA 4.3 2.7 - - - -
1078D LEU* 5.5 0.4 - - - +
1111D ASP* 5.5 12.4 - - + +
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Residues in contact with THR1038 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036D ARG* 4.3 4.9 - - - -
1037D PHE* 1.3 74.5 - - - +
1039D ASP* 1.3 68.0 + - - +
1040D MET* 3.4 5.3 + - - +
1076D PRO* 3.7 0.5 - - - +
1077D ALA* 3.0 53.1 + - - +
1079D LYS* 4.3 12.6 - - - -
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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