Contacts of the helix formed by residues 616 - 632 (chain R) in PDB entry 6CNC
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 ASN 616 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414R HIS* 3.5 2.0 + - - -
614R LEU* 4.0 4.6 + - - -
615R LEU* 1.3 97.4 - - - +
617R GLU* 1.3 64.2 + - - +
618R GLU* 3.0 12.4 + - - +
619R ALA* 2.4 41.4 + - - +
620R SER 3.4 0.9 + - - -
478S PRO* 6.0 4.4 - - - +
479S PRO* 6.2 1.6 - - - +
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Residues in contact with GLU 617 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414R HIS* 3.7 17.0 + - + +
616R ASN* 1.3 75.7 - - - +
618R GLU* 1.3 58.2 + - - +
620R SER* 3.1 5.9 + - - -
621R LYS* 2.9 60.5 + - + +
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Residues in contact with GLU 618 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616R ASN* 3.0 11.8 + - - +
617R GLU* 1.3 76.9 - - - +
619R ALA* 1.3 60.6 + - - +
621R LYS* 2.8 34.5 + - + +
622R LEU* 2.9 25.2 + - + +
483S GLU* 5.7 4.1 - - - +
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Residues in contact with ALA 619 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615R LEU* 3.7 27.4 - - + -
616R ASN* 2.4 35.7 + - - +
618R GLU* 1.3 68.8 - - - +
620R SER* 1.3 51.4 + - - +
623R LYS* 2.4 49.1 + - - +
479S PRO* 6.0 7.6 - - + -
483S GLU* 4.9 9.2 - - - +
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Residues in contact with SER 620 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413R LEU* 3.1 42.4 - - - +
414R HIS* 3.4 27.5 - - - -
615R LEU* 3.4 6.8 - - - +
617R GLU* 3.1 9.8 + - - -
618R GLU 3.1 0.4 - - - -
619R ALA* 1.3 77.9 - - - +
621R LYS* 1.3 59.2 + - - +
623R LYS* 4.3 1.8 - - - -
624R GLU* 2.8 36.4 + - - +
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Residues in contact with LYS 621 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617R GLU* 2.9 51.5 + - + +
618R GLU* 2.8 23.0 + - + +
620R SER* 1.3 77.4 - - - +
622R LEU* 1.3 56.7 + - - +
624R GLU* 3.9 3.8 - - - +
625R ARG* 2.9 26.6 + - - +
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Residues in contact with LEU 622 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618R GLU* 2.9 20.6 + - + +
621R LYS* 1.3 73.4 - - - +
623R LYS* 1.3 61.3 + - - +
625R ARG* 3.2 16.1 + - + +
626R ILE* 2.9 43.3 + - + +
435S TRP* 4.9 0.7 - - - +
483S GLU* 3.2 36.6 - - + +
484S TYR* 5.9 3.1 - - + -
487S GLU* 3.3 40.8 - - - +
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Residues in contact with LYS 623 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412R ALA 5.3 5.4 - - - +
413R LEU 4.7 5.6 - - - +
415R ALA 4.2 4.4 + - - +
416R ARG 5.8 0.2 + - - -
615R LEU* 3.2 32.6 - - + +
619R ALA* 2.4 41.6 + - - +
620R SER* 4.3 1.1 - - - -
622R LEU* 1.3 76.9 - - - +
624R GLU* 1.3 59.0 + - - +
626R ILE* 3.0 12.0 + - - +
627R TRP* 2.9 26.2 + - + +
435S TRP* 3.3 58.2 + - + +
438S ASP* 5.9 3.8 - - + +
441S LEU* 4.8 10.7 - - + +
483S GLU* 5.1 0.6 + - - +
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Residues in contact with GLU 624 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409R LYS* 3.3 25.0 + - - -
413R LEU* 3.3 40.2 - - + +
620R SER* 2.8 24.3 + - - +
621R LYS* 4.0 3.8 - - - +
623R LYS* 1.3 72.7 - - - +
625R ARG* 1.3 59.5 + - - +
627R TRP* 4.0 7.4 - - + -
628R ILE* 2.9 48.8 + - + +
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Residues in contact with ARG 625 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621R LYS 2.9 17.6 + - - +
622R LEU* 3.2 22.2 - - - +
623R LYS 3.2 0.4 - - - -
624R GLU* 1.3 75.5 - - - +
626R ILE* 1.3 55.9 + - - +
628R ILE* 5.2 0.4 - - - -
629R GLY* 2.9 19.8 + - - -
487S GLU* 4.8 10.3 + - - +
492S ILE* 3.3 14.4 + - + +
494S THR* 3.3 30.3 - - - +
495S VAL* 3.2 51.1 - - + +
496S ALA* 3.9 11.7 - - - +
497S ASP* 5.4 1.4 - - - +
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Residues in contact with ILE 626 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622R LEU* 2.9 36.2 + - + +
623R LYS* 3.0 7.8 + - - +
625R ARG* 1.3 76.1 - - - +
627R TRP* 1.3 66.5 + - - +
629R GLY* 3.0 1.0 + - - -
630R LEU* 2.9 36.3 + - + +
435S TRP* 4.0 23.8 - - + +
441S LEU* 3.9 33.4 - - + -
444S GLN* 6.0 1.1 - - + -
487S GLU* 3.9 26.0 - - + +
492S ILE* 3.7 13.2 - - + +
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Residues in contact with TRP 627 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409R LYS* 3.5 36.8 - - + -
412R ALA* 5.5 5.4 - - + +
413R LEU* 6.5 0.2 - - + -
420R TYR* 2.6 61.6 + + + +
422R PRO* 4.5 5.8 - - + -
623R LYS* 2.9 14.2 + - + +
624R GLU* 3.6 11.7 - - + +
626R ILE* 1.3 78.3 - - - +
628R ILE* 1.3 87.6 + - + +
630R LEU* 3.1 2.3 + - - +
631R ASN* 2.3 69.5 + - + +
634R PHE* 5.7 5.4 - + - -
635R LEU* 5.6 10.3 - - + -
438S ASP* 5.6 5.6 - - - -
440S ASN* 5.8 4.7 - - - +
441S LEU* 5.4 7.8 - - + +
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Residues in contact with ILE 628 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409R LYS* 3.3 23.3 - - - +
624R GLU* 2.9 35.8 + - + +
625R ARG* 5.8 0.2 - - - -
627R TRP* 1.3 94.0 - - + +
629R GLY* 1.3 63.5 + - - +
631R ASN* 4.1 3.6 - - - +
632R ALA* 2.9 29.4 + - + +
635R LEU* 5.5 11.4 - - + -
495S VAL* 3.8 9.0 - - + -
496S ALA* 6.4 0.4 - - + -
499S ASN* 3.2 43.3 - - - +
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Residues in contact with GLY 629 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625R ARG 2.9 21.1 + - - -
626R ILE 3.0 6.4 + - - -
628R ILE* 1.3 78.4 - - - +
630R LEU* 1.3 61.0 + - - +
632R ALA* 4.4 6.6 + - - +
492S ILE* 4.1 18.0 - - - +
495S VAL* 3.5 16.1 - - - +
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Residues in contact with LEU 630 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626R ILE* 2.9 26.5 + - + +
627R TRP* 3.9 5.6 - - - +
629R GLY* 1.3 78.4 - - - +
631R ASN* 1.3 65.6 + - - +
632R ALA 3.4 1.9 + - - -
633R ASP* 4.4 10.8 + - - +
634R PHE 5.1 0.3 + - - -
440S ASN* 3.9 16.8 - - - +
441S LEU* 5.4 2.5 - - + -
444S GLN* 3.3 49.1 - - + +
490S LYS* 3.9 15.7 - - + +
492S ILE* 4.7 9.4 - - + -
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Residues in contact with ASN 631 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421R ASN* 3.4 22.9 - - - +
422R PRO* 5.4 0.2 - - - +
627R TRP* 2.3 88.6 + - + +
628R ILE* 3.1 3.5 + - - -
630R LEU* 1.3 80.9 - - - +
632R ALA* 1.3 61.1 + - - +
633R ASP 3.1 3.1 - - - -
634R PHE* 3.0 17.1 + - + +
635R LEU* 2.9 30.8 + - + +
440S ASN* 5.2 7.4 + - - +
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Residues in contact with ALA 632 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628R ILE* 2.9 18.0 + - - +
629R GLY* 4.6 6.5 - - - +
630R LEU 3.4 1.8 - - - -
631R ASN* 1.3 78.0 - - - +
633R ASP* 1.3 54.0 + - - +
635R LEU* 4.8 4.7 - - - -
636R LEU* 2.6 37.8 + - - +
498S PHE* 4.6 22.0 - - + -
499S ASN* 4.2 16.4 - - - +
502S LEU* 4.1 8.1 - - + +
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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
------------------------------------------------------------
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