Contacts of the helix formed by residues 658 - 669 (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 ASP 658 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590B THR* 5.5 5.5 + - - +
656B SER 4.0 0.2 + - - -
657B LEU* 1.3 76.2 - - - +
659B LYS* 1.3 67.1 + - - +
660B TRP* 2.9 11.1 + - - +
661B GLU* 2.5 58.9 + - - +
662B ARG* 2.9 21.4 + - - +
801B PCG 4.3 14.6 + - - +
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Residues in contact with LYS 659 (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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645B GLU* 5.8 8.5 - - - -
658B ASP* 1.3 72.6 - - - +
660B TRP* 1.3 59.7 + - - +
662B ARG* 3.0 41.3 + - + +
663B LEU* 3.2 28.8 + - + +
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Residues in contact with TRP 660 (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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590B THR* 6.1 3.1 - - + -
592B VAL* 4.2 18.2 - - + -
597B SER* 3.4 26.2 - - - -
600B GLU* 3.1 26.4 + - - -
601B LEU* 3.9 17.7 - - + -
641B ARG* 4.6 3.6 - - - +
658B ASP* 2.9 11.2 + - - +
659B LYS* 1.3 73.6 - - - +
661B GLU* 1.3 74.9 + - + +
662B ARG 3.1 0.2 + - - -
663B LEU* 3.2 21.9 + - + +
664B THR* 2.8 50.2 + - + -
801B PCG 3.2 78.2 + + + +
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Residues in contact with GLU 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B THR* 5.0 12.5 - - + +
656B SER 4.6 1.4 - - - +
657B LEU* 3.4 32.2 - - + +
658B ASP* 2.5 51.8 + - - +
660B TRP* 1.3 81.3 - - + +
662B ARG* 1.3 61.6 + - - +
664B THR* 3.1 12.9 - - + +
665B VAL* 3.0 25.3 + - - +
756B VAL 4.4 1.3 - - - +
759B PRO* 3.4 26.7 - - - +
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Residues in contact with ARG 662 (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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645B GLU* 4.3 8.7 - - - +
648B LEU* 3.8 41.1 + - + +
649B SER* 4.0 19.7 - - - +
654B LEU* 3.2 27.7 + - + +
655B GLU* 4.1 6.3 + - - +
657B LEU* 2.7 32.9 + - - +
658B ASP 2.9 13.5 + - - -
659B LYS* 3.0 29.6 - - + +
660B TRP 3.0 0.2 - - - -
661B GLU* 1.3 73.2 - - - +
663B LEU* 1.3 61.0 + - + +
665B VAL* 2.7 31.3 + - - +
666B ALA 3.0 8.5 + - - -
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Residues in contact with LEU 663 (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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601B LEU* 5.6 2.2 - - + -
641B ARG* 3.7 54.1 - - + +
645B GLU* 5.5 11.4 - - + +
659B LYS* 3.5 25.8 - - + +
660B TRP* 3.4 36.1 - - + +
662B ARG* 1.3 76.3 - - + +
664B THR* 1.3 52.3 + - - +
666B ALA* 2.6 30.6 + - + +
667B ASP* 2.7 22.1 + - - +
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Residues in contact with THR 664 (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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641B ARG* 5.9 0.2 - - - +
660B TRP* 2.8 46.3 + - + -
661B GLU* 3.1 18.2 - - + +
663B LEU* 1.3 76.2 - - - +
665B VAL* 1.3 60.1 + - - +
667B ASP* 3.5 13.1 + - - +
668B ALA* 3.1 16.3 + - - +
755B ARG* 5.1 7.8 + - + +
756B VAL* 3.3 31.7 - - + +
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Residues in contact with VAL 665 (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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648B LEU* 4.2 20.0 - - + -
654B LEU* 5.0 8.1 - - + -
657B LEU* 3.6 9.4 - - + -
661B GLU 3.0 15.3 + - - +
662B ARG* 2.7 14.1 + - - +
664B THR* 1.3 69.4 - - - +
666B ALA* 1.3 69.4 + - - +
668B ALA* 3.1 5.2 + - - +
669B LEU* 3.0 35.5 + - + +
692B ILE* 5.7 4.0 - - + -
748B LEU* 4.9 2.9 - - + +
756B VAL* 3.5 21.3 - - + +
757B LEU* 3.3 35.9 - - + -
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Residues in contact with ALA 666 (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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640B LYS* 3.3 19.5 + - + +
641B ARG* 4.6 9.4 - - - +
644B TYR* 4.3 13.9 - - + -
648B LEU* 3.9 10.5 - - + +
662B ARG 3.0 6.4 + - - +
663B LEU* 2.6 26.9 + - + +
665B VAL* 1.3 71.1 - - - +
667B ASP* 1.3 56.1 + - - +
669B LEU* 2.6 44.4 + - - +
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Residues in contact with ASP 667 (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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534B VAL* 3.3 13.3 - - - +
535B LEU* 3.7 39.3 + - + +
597B SER* 5.1 4.3 + - - -
637B THR* 4.7 5.1 - - - +
640B LYS* 3.3 18.2 + - - +
641B ARG* 3.3 45.2 + - - +
663B LEU 2.7 17.5 + - - +
664B THR* 3.6 13.9 + - - +
666B ALA* 1.3 73.7 - - - +
668B ALA* 1.3 61.3 + - - +
669B LEU 3.2 0.7 + - - -
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Residues in contact with ALA 668 (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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534B VAL* 3.8 7.3 - - - +
664B THR 3.1 2.6 + - - +
665B VAL 3.1 4.6 + - - +
666B ALA 3.0 1.0 - - - -
667B ASP* 1.3 77.8 - - - +
669B LEU* 1.3 58.7 + - - +
748B LEU* 3.9 4.3 - - + +
752B ARG* 2.8 51.8 + - + +
755B ARG* 4.1 5.6 - - - +
756B VAL* 3.5 33.9 - - + -
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Residues in contact with LEU 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 3.5 5.1 - - - +
640B LYS* 2.7 34.6 + - - -
644B TYR* 3.9 28.3 - - + -
647B PHE* 6.0 0.2 - - + -
648B LEU* 4.2 16.4 - - + -
665B VAL* 3.0 24.4 + - + +
666B ALA* 2.6 35.1 + - - +
667B ASP 3.2 0.4 - - - -
668B ALA* 1.3 70.8 - - - +
670B GLU* 1.3 58.6 + - - +
671B PRO* 3.3 4.4 - - - +
692B ILE* 5.1 7.2 - - + -
746B VAL* 3.7 35.0 - - + +
747B LYS 4.0 1.8 - - - +
748B LEU* 3.6 22.2 - - + -
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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