Contacts of the helix formed by residues 613 - 633 (chain W) in PDB entry 6NE3
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 VAL 613 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I G 5.3 2.5 - - - +
450W LEU* 3.4 56.8 - - + +
453W LEU* 4.6 4.6 - - + +
454W ARG* 4.3 4.3 - - + -
581W TRP* 5.1 3.8 - - + -
612W THR* 1.3 84.2 + - - +
614W GLU* 1.3 57.3 + - - +
615W GLU 3.3 3.1 - - - -
616W ARG* 3.0 21.7 + - + -
617W ILE* 2.9 40.5 + - + +
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Residues in contact with GLU 614 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454W ARG* 3.7 24.1 - - + +
457W CYS* 3.3 17.8 - - + +
458W ASN* 4.8 0.2 - - - +
484W LYS* 3.7 15.6 + - - -
578W ASP* 3.9 12.5 - - - +
608W ILE* 3.7 18.8 - - + +
609W THR* 2.5 39.3 + - - +
612W THR* 3.4 16.5 - - + +
613W VAL* 1.3 76.2 - - + +
615W GLU* 1.3 60.6 + - - +
617W ILE* 3.2 21.0 + - + +
618W VAL* 3.0 29.6 + - - +
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Residues in contact with GLU 615 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608W ILE* 4.3 4.9 - - + +
609W THR 3.0 21.2 - - - +
610W ASP* 3.1 21.0 - - - +
611W ASN* 2.8 11.4 + - - -
612W THR* 2.7 42.4 + - - +
614W GLU* 1.3 76.1 - - - +
616W ARG* 1.3 78.8 + - - +
618W VAL* 3.3 11.2 - - + +
619W GLU* 2.9 34.5 + - + +
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Residues in contact with ARG 616 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581W TRP* 4.1 6.2 - - + -
612W THR 4.7 2.0 - - - +
613W VAL* 3.0 29.0 + - + +
615W GLU* 1.3 91.3 - - + +
617W ILE* 1.3 60.2 + - - +
619W GLU* 3.8 22.5 - - - +
620W ARG* 2.9 34.7 + - - +
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Residues in contact with ILE 617 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454W ARG* 3.7 39.5 - - + +
578W ASP* 5.3 1.1 - - - +
579W SER* 3.4 24.5 - - - +
580W ASP 3.5 18.8 - - - +
581W TRP* 3.6 37.5 - - + -
613W VAL* 2.9 17.2 + - + +
614W GLU* 3.2 26.0 + - + +
616W ARG* 1.3 76.7 - - - +
618W VAL* 1.3 61.8 + - + +
620W ARG* 3.8 1.9 - - - +
621W ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 618 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411W LYS* 5.4 10.5 - - - +
579W SER* 4.3 13.9 - - - +
606W ARG* 3.6 29.6 - - - +
608W ILE* 4.1 18.8 - - + -
614W GLU 3.0 16.1 + - - +
615W GLU* 3.3 20.0 - - + +
617W ILE* 1.3 78.5 - - + +
619W GLU* 1.3 59.2 + - + +
621W ALA* 3.7 6.6 - - - +
622W GLU* 2.8 41.9 + - + +
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Residues in contact with GLU 619 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615W GLU* 2.9 21.8 + - + +
616W ARG* 3.8 27.1 - - - +
618W VAL* 1.3 77.2 - - + +
620W ARG* 1.3 61.4 + - - +
622W GLU* 3.0 29.8 + - - +
623W MET* 3.0 38.8 + - + +
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Residues in contact with ARG 620 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I T 3.4 22.2 - - - -
157I G 2.8 36.6 + - - -
581W TRP* 3.9 29.6 - - + +
616W ARG* 2.9 21.2 + - - +
619W GLU* 1.3 74.9 - - - +
621W ALA* 1.3 57.1 + - - +
623W MET* 3.3 21.7 + - + +
624W LYS* 2.9 46.6 + - + +
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Residues in contact with ALA 621 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579W SER* 4.8 5.6 - - - +
580W ASP 4.6 7.4 - - - +
581W TRP 4.5 7.5 + - - +
583W PRO* 3.4 38.3 - - + +
617W ILE 2.9 18.6 + - - +
618W VAL* 3.7 9.6 - - - +
620W ARG* 1.3 76.6 - - - +
622W GLU* 1.3 56.3 + - - +
624W LYS* 4.4 0.2 - - - -
625W LEU* 2.8 31.3 + - - +
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Residues in contact with GLU 622 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618W VAL* 2.8 30.7 + - + +
619W GLU* 3.0 32.5 + - - +
621W ALA* 1.3 75.6 - - - +
623W MET* 1.3 60.5 + - + +
625W LEU* 3.7 13.6 - - + +
626W ARG* 2.8 28.4 + - - +
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Residues in contact with MET 623 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619W GLU* 3.0 24.5 + - - +
620W ARG* 3.3 25.3 + - + +
622W GLU* 1.3 74.8 - - + +
624W LYS* 1.3 59.0 + - + +
626W ARG* 3.2 6.8 + - - +
627W LEU* 3.0 36.5 + - + +
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Residues in contact with LYS 624 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I G 5.4 2.2 + - - -
156I T 3.3 23.7 + - - -
341W GLN 4.8 6.5 - - - +
342W ASN* 2.4 41.4 + - - +
581W TRP 4.3 10.4 + - - +
582W ASN* 5.1 3.8 - - - +
583W PRO* 3.9 24.9 - - + -
584W GLN* 5.3 3.1 - - - +
620W ARG* 2.9 34.3 + - + +
621W ALA 3.7 4.3 - - - +
623W MET* 1.3 76.8 - - + +
625W LEU* 1.3 56.2 + - - +
627W LEU* 3.4 20.5 - - + +
628W ASP* 2.9 29.7 + - - +
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Residues in contact with LEU 625 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583W PRO* 4.1 20.6 - - + +
584W GLN* 6.4 0.4 - - - -
587W LEU* 4.6 24.0 - - + -
621W ALA 2.8 17.2 + - - +
622W GLU* 3.7 12.8 - - + +
624W LYS* 1.3 76.5 - - - +
626W ARG* 1.3 60.5 + - - +
628W ASP* 3.6 7.5 - - - +
629W SER* 2.8 36.6 + - - -
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Residues in contact with ARG 626 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622W GLU 2.8 17.9 + - - +
623W MET* 3.2 8.7 + - - +
625W LEU* 1.3 78.8 - - - +
627W LEU* 1.3 58.9 + - - +
629W SER* 2.9 29.8 + - - -
630W ILE* 3.0 43.5 + - + +
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Residues in contact with LEU 627 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340W LEU* 4.3 11.8 - - + +
342W ASN 3.3 26.9 - - - +
343W ASN* 4.8 6.3 - - + +
623W MET* 3.0 22.1 + - + +
624W LYS* 3.4 25.4 - - + +
626W ARG* 1.3 76.7 - - - +
628W ASP* 1.3 59.2 + - - +
630W ILE* 4.3 12.2 + - - +
631W VAL* 3.5 18.4 + - - +
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Residues in contact with ASP 628 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338W THR* 5.6 2.3 - - - -
340W LEU* 3.5 31.9 + - + +
584W GLN* 3.2 31.7 - - + +
587W LEU* 6.5 0.9 - - - -
624W LYS 2.9 18.0 + - - +
625W LEU* 3.7 9.4 - - + +
626W ARG 3.1 0.2 - - - -
627W LEU* 1.3 77.9 - - - +
629W SER* 1.3 57.2 + - - +
631W VAL* 3.3 4.2 - - - +
632W ILE* 2.8 46.6 + - - +
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Residues in contact with SER 629 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625W LEU* 2.8 25.0 + - - -
626W ARG* 2.9 23.1 + - - -
628W ASP* 1.3 76.3 - - - +
630W ILE* 1.3 65.3 + - - +
632W ILE* 3.7 10.5 - - - -
633W GLN* 3.0 41.9 + - - +
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Residues in contact with ILE 630 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380W LEU* 5.7 6.3 - - + -
381W VAL* 5.0 16.7 - - + +
384W LEU* 4.6 4.9 - - - +
626W ARG* 3.0 46.9 + - + +
627W LEU* 4.3 10.3 + - + +
628W ASP 3.4 0.2 - - - -
629W SER* 1.3 76.9 - - - +
631W VAL* 1.3 62.6 + - + +
633W GLN* 4.4 9.9 + - - +
634W GLN* 5.1 0.7 + - - +
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Residues in contact with VAL 631 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340W LEU* 4.3 12.8 - - + -
380W LEU* 4.2 31.6 - - + +
381W VAL* 5.5 0.4 - - + -
384W LEU* 3.3 44.2 - - + +
627W LEU 3.5 16.6 - - - +
628W ASP* 3.3 15.9 - - - +
630W ILE* 1.3 82.2 - - + +
632W ILE* 1.3 65.0 + - + +
633W GLN 3.3 0.9 - - - -
634W GLN 3.7 4.2 + - - -
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Residues in contact with ILE 632 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339W PRO* 4.9 14.8 - - + -
340W LEU* 6.0 3.6 - - + -
394W ARG* 3.4 56.1 + - + +
628W ASP* 2.8 33.6 + - - +
629W SER* 3.1 14.7 + - - +
631W VAL* 1.3 78.7 - - + +
633W GLN* 1.3 75.1 + - - +
634W GLN 3.2 8.8 + - - +
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Residues in contact with GLN 633 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629W SER* 3.0 30.9 + - - +
630W ILE* 4.6 8.5 - - - +
631W VAL 3.3 0.8 - - - -
632W ILE* 1.3 87.2 - - - +
634W GLN* 1.3 57.6 + - + +
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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