Contacts of the strand formed by residues 829 - 834 (chain B) in PDB entry 3RMD
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 LYS 829 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284B ASN* 3.9 12.3 + - - +
285B GLN 3.5 16.2 - - - +
286B PRO* 3.1 34.3 - - + +
287B SER* 5.0 2.0 - - - -
288B TYR* 5.2 8.5 - - + -
735B SER* 4.0 14.8 + - - -
736B SER 5.5 0.4 - - - +
782B VAL* 4.2 11.3 - - + +
783B SER 3.0 9.0 - - - +
784B SER* 3.3 19.3 + - - +
827B GLY 5.3 0.7 - - - +
828B GLU* 1.3 79.3 - - - +
830B VAL* 1.3 67.2 + - - +
849B PRO* 4.1 2.3 - - - +
850B SER* 3.2 22.6 + - - +
112H T 2.6 34.5 + - - -
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Residues in contact with VAL 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782B VAL* 3.4 3.1 - - - +
783B SER 2.6 43.1 + - - +
785B ALA* 4.2 7.9 - - + -
804B HIS* 4.5 6.5 - - + +
808B ILE* 3.9 16.2 - - + -
824B VAL* 3.8 33.0 - - + -
825B VAL 5.7 0.2 - - - +
828B GLU 4.6 1.6 - - - +
829B LYS* 1.3 81.1 - - - +
831B TYR* 1.3 62.1 + - - +
832B VAL* 3.8 10.6 + - + +
847B ALA* 3.7 22.2 - - + -
848B TRP 3.3 15.5 - - - +
849B PRO* 4.6 1.3 - - + -
850B SER* 3.8 6.1 - - - +
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Residues in contact with TYR 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B PRO* 5.1 4.5 - - + +
287B SER* 5.9 0.2 - - - -
292B TYR* 4.4 13.0 + - - -
739B LYS* 5.9 2.4 - - - +
777B ILE* 3.6 37.2 - - + +
780B ALA* 4.0 11.7 - - + -
781B SER 3.2 12.1 - - - -
782B VAL* 3.6 23.3 - - + -
830B VAL* 1.3 73.7 - - - +
832B VAL* 1.3 59.7 + - - +
847B ALA* 3.0 8.5 - - - +
848B TRP* 2.8 75.2 + + + +
850B SER* 3.7 15.7 - - - -
851B GLY* 3.2 31.5 + - - -
852B THR 4.1 6.1 - - - -
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Residues in contact with VAL 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780B ALA* 3.8 0.7 - - - -
781B SER* 2.8 42.5 + - - +
783B SER* 5.0 3.8 - - - -
803B PHE* 4.3 26.9 - - + -
804B HIS* 3.9 19.7 - - + -
830B VAL* 3.8 15.3 - - + +
831B TYR* 1.3 81.8 - - - +
833B LEU* 1.3 74.6 + - - +
834B PRO* 4.7 2.1 - - + +
845B CYS* 4.5 11.2 - - + -
846B ILE 3.8 10.3 - - - +
847B ALA* 3.6 14.8 - - + -
848B TRP* 4.6 0.2 - - - -
871B LEU* 4.8 1.4 - - - +
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Residues in contact with LEU 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776B TYR* 3.8 15.3 - - + +
779B ILE* 4.5 1.3 - - + -
780B ALA* 3.6 27.1 - - + -
832B VAL* 1.3 78.0 - - - +
834B PRO* 1.3 74.8 - - + +
835B LEU* 4.4 0.4 - - + +
845B CYS* 3.4 4.1 - - - +
846B ILE* 3.2 31.7 + - + +
848B TRP* 3.5 28.0 - - + -
862B VAL* 4.2 11.0 - - + -
866B MET* 3.6 33.9 - - + -
871B LEU* 3.6 29.8 - - + -
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Residues in contact with PRO 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B PHE* 4.8 13.7 - - + -
832B VAL* 4.7 1.6 - - + +
833B LEU* 1.3 89.2 - - + +
835B LEU* 1.3 57.7 + - - +
844B LYS 3.5 9.4 - - - +
845B CYS* 3.9 3.8 - - + -
866B MET* 3.1 9.4 - - + +
867B ASP* 2.8 51.2 + - + +
870B VAL* 4.0 16.8 - - + -
871B LEU* 3.5 34.8 - - + +
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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