Contacts of the helix formed by residues 750 - 757 (chain B) in PDB entry 1RL3
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 ARG 750 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687B GLY 3.6 10.1 + - - -
688B ASP* 2.8 55.2 + - - +
726B ALA 4.0 13.7 + - - -
727B LEU* 3.5 30.5 - - + +
730B ASN* 6.2 0.4 - - - +
749B ASP* 1.3 69.9 - - - +
751B PRO* 1.3 66.9 - - + +
753B PHE* 4.2 1.3 - - - -
754B GLU* 2.9 64.2 + - + +
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Residues in contact with PRO 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LYS* 6.1 5.8 - - + +
594B GLU 5.7 0.6 - - - +
688B ASP* 5.7 0.2 - - - +
749B ASP* 3.0 23.1 - - + +
750B ARG* 1.3 97.0 - - + +
752B ARG* 1.3 65.3 + - + +
754B GLU* 3.5 8.7 + - - +
755B ARG* 3.1 26.7 + - - +
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Residues in contact with ARG 752 (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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532B LYS 4.7 14.9 + - - +
534B VAL* 3.9 13.2 - - - +
668B ALA* 2.8 40.1 + - + +
670B GLU* 3.5 27.3 + - - +
747B LYS 3.4 19.0 + - - -
748B LEU* 3.8 8.1 - - + +
749B ASP* 3.0 48.4 + - - +
751B PRO* 1.3 76.1 - - + +
753B PHE* 1.3 61.3 + - - +
755B ARG* 3.6 34.8 - - - +
756B VAL* 2.5 37.8 + - - +
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Residues in contact with PHE 753 (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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690B PHE* 3.7 29.6 - + + -
724B GLU* 4.3 12.3 - - + -
727B LEU* 3.2 53.4 - - + -
728B LEU* 4.4 11.7 - - + -
748B LEU* 3.8 16.7 - - + +
749B ASP 2.8 22.1 + - - +
750B ARG 3.5 1.1 - - - +
752B ARG* 1.3 78.4 - - - +
754B GLU* 1.3 72.2 + - + +
755B ARG 2.8 10.2 + - - -
757B LEU* 3.1 38.8 + - + +
764B LEU* 3.9 27.6 - - + -
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Residues in contact with GLU 754 (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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727B LEU 4.7 5.9 - - - +
728B LEU* 6.5 0.2 - - + -
750B ARG* 2.9 57.9 + - + +
751B PRO* 3.9 6.0 - - - +
753B PHE* 1.3 87.5 - - + +
755B ARG* 1.3 56.8 + - - +
758B GLY* 3.7 17.4 - - - +
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Residues in contact with ARG 755 (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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533B ASN* 5.9 1.0 - - - +
592B VAL* 6.0 0.2 - - - -
593B GLY* 4.2 16.6 - - - +
594B GLU 3.7 18.8 + - - +
595B GLY* 3.5 30.8 + - - -
596B GLY* 3.7 18.6 - - - +
664B THR* 5.1 6.6 + - + +
668B ALA* 4.1 5.5 - - - +
751B PRO* 3.1 20.5 + - - +
752B ARG* 2.9 40.0 + - - +
753B PHE 2.8 3.0 + - - -
754B GLU* 1.3 78.8 - - - +
756B VAL* 1.3 86.8 + - - +
757B LEU 3.0 1.3 - - - -
758B GLY* 3.1 11.8 + - - -
759B PRO* 4.3 4.0 - - - +
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Residues in contact with VAL 756 (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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657B LEU* 3.3 27.7 - - - +
661B GLU* 4.4 1.6 - - - +
664B THR* 3.3 41.0 - - + +
665B VAL* 3.5 17.6 - - + +
668B ALA* 3.5 17.0 - - + -
748B LEU* 3.5 20.0 - - + -
752B ARG 2.5 28.9 + - - +
755B ARG* 1.3 83.9 - - - +
757B LEU* 1.3 74.7 + - + +
758B GLY 3.9 0.3 + - - -
759B PRO* 4.5 2.1 - - - +
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Residues in contact with LEU 757 (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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654B LEU* 4.2 13.9 - - + -
657B LEU* 4.9 0.2 - - + -
665B VAL* 3.3 37.7 - - + -
690B PHE* 3.2 43.1 - - + -
692B ILE* 5.7 0.7 - - + -
748B LEU* 3.4 12.6 - - + -
753B PHE* 3.1 27.9 + - + +
754B GLU* 5.3 0.2 - - - -
755B ARG 3.0 0.6 - - - -
756B VAL* 1.3 85.7 - - + +
758B GLY* 1.3 64.2 + - - +
759B PRO* 3.3 3.1 - - - -
760B CYS* 2.9 36.0 + - + +
761B SER* 3.5 3.8 + - - -
764B LEU* 4.7 3.4 - - + +
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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
------------------------------------------------------------
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