Contacts of the strand formed by residues 829 - 834 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C ASN* 2.8 35.4 - - - +
285C GLN 3.1 18.8 + - - +
286C PRO* 3.1 31.2 - - + +
287C SER* 5.2 1.8 - - - -
288C TYR* 4.8 11.0 - - + -
735C SER* 3.9 8.1 + - - -
782C VAL* 4.1 9.8 - - + +
783C SER 3.1 9.4 - - - +
784C SER* 3.4 25.4 - - - +
827C GLY 4.9 1.1 - - - +
828C GLU* 1.3 83.4 - - - +
830C VAL* 1.3 65.9 + - - +
849C PRO* 4.1 1.6 - - - +
850C SER* 3.0 23.5 + - - +
112J T 4.1 9.6 + - - +
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Residues in contact with VAL 830 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782C VAL* 3.2 4.7 - - - -
783C SER* 2.7 46.0 + - - +
785C ALA* 4.3 8.7 - - + -
804C HIS* 4.9 4.9 - - + +
808C ILE* 3.3 36.8 - - + -
824C VAL* 3.6 17.7 - - + -
828C GLU 4.8 0.7 - - - +
829C LYS* 1.3 81.0 - - - +
831C TYR* 1.3 62.7 + - - +
832C VAL* 3.8 9.0 - - + +
847C ALA* 3.9 11.0 - - + -
848C TRP 3.3 18.4 - - - +
849C PRO* 4.4 1.1 - - + -
850C SER* 3.9 6.1 - - - +
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Residues in contact with TYR 831 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PRO* 5.1 4.0 - - + +
292C TYR* 4.1 13.2 + - - -
777C ILE* 3.6 31.4 - - + +
780C ALA* 4.2 13.0 - - + -
781C SER 3.1 8.1 - - - -
782C VAL* 3.4 28.7 - - + -
830C VAL* 1.3 73.4 - - - +
832C VAL* 1.3 59.3 + - - +
847C ALA* 3.0 26.5 - - - +
848C TRP* 2.8 55.5 + + + +
850C SER* 3.5 13.9 - - - -
851C GLY* 2.9 35.5 + - - -
852C THR 3.6 13.2 - - - -
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Residues in contact with VAL 832 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C ALA* 3.8 0.2 - - - +
781C SER* 2.7 44.9 + - - +
783C SER* 4.5 6.3 - - - -
803C PHE* 4.0 30.7 - - + -
804C HIS* 4.1 19.1 - - + -
830C VAL* 3.8 16.8 - - + +
831C TYR* 1.3 83.5 - - - +
833C LEU* 1.3 75.4 + - - +
834C PRO* 4.5 1.5 - - + +
845C CYS* 4.8 4.5 - - + -
846C ILE 3.9 6.1 - - - +
847C ALA* 3.8 14.1 - - + -
871C LEU* 4.7 0.3 - - - +
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Residues in contact with LEU 833 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776C TYR* 4.2 13.5 - - + +
780C ALA* 3.7 23.3 - - + +
803C PHE* 5.6 0.2 - - - -
832C VAL* 1.3 85.4 - - - +
834C PRO* 1.3 72.0 - - + +
845C CYS* 3.3 4.7 - - - +
846C ILE* 3.0 41.7 + - + +
848C TRP* 3.7 28.0 - - + -
862C VAL* 4.4 11.2 - - + -
866C MET* 4.0 31.9 - - + -
871C LEU* 4.0 24.2 - - + -
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Residues in contact with PRO 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803C PHE* 4.6 3.1 - - + -
832C VAL* 4.5 0.9 - - + +
833C LEU* 1.3 90.1 - - + +
835C LEU* 1.3 61.7 + - - +
844C LYS 3.5 9.6 - - - +
845C CYS* 3.9 2.9 - - + -
866C MET* 3.2 9.1 - - + +
867C ASP* 2.9 46.2 + - + +
870C VAL* 4.4 6.5 - - + -
871C LEU* 3.5 35.0 - - + +
874C LYS* 4.0 24.5 - - - +
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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