Contacts of the helix formed by residues 616 - 634 (chain A) in PDB entry 6NFJ
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PRO* 6.2 0.4 - - - +
605A SER 3.3 25.7 + - - +
606A VAL* 3.1 17.6 + - - +
608A PRO* 5.0 9.1 - - + +
614A ALA 4.0 0.8 - - - -
615A VAL* 1.3 69.4 - - - +
617A ARG* 1.3 61.6 + - - +
618A GLN* 3.1 14.4 + - - +
619A ALA* 2.9 38.0 + - + +
620A LEU* 3.2 15.4 + - - +
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Residues in contact with ARG 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A VAL* 2.8 18.5 + - + +
616A ASN* 1.3 73.1 - - - +
618A GLN* 1.3 57.3 + - - +
620A LEU* 4.0 7.6 - - - +
621A ARG* 3.1 26.9 + - - +
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Residues in contact with GLN 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ASN* 3.1 9.9 + - - +
617A ARG* 1.3 77.7 - - - +
619A ALA* 1.3 59.4 + - - +
621A ARG* 3.3 6.9 + - + +
622A TYR* 3.0 27.6 + - + +
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Residues in contact with ALA 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PRO* 4.6 18.6 - - + -
605A SER* 3.6 16.4 - - - +
606A VAL* 4.0 11.9 - - + -
616A ASN* 2.9 30.6 + - + +
618A GLN* 1.3 77.7 - - - +
620A LEU* 1.3 60.1 + - - +
622A TYR* 3.3 7.9 + - - +
623A TYR* 3.2 31.9 + - + -
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A VAL* 3.9 31.2 - - + -
615A VAL* 4.2 14.4 - - + -
616A ASN 3.2 7.1 + - - +
617A ARG* 4.1 5.6 - - - +
619A ALA* 1.3 74.8 - - - +
621A ARG* 1.3 60.5 + - - +
623A TYR* 3.6 13.1 + - + +
624A ARG* 3.1 26.2 + - - +
676A LEU* 4.1 27.1 - - + -
677A CYS* 4.5 17.0 - - - -
680A GLU* 4.3 25.0 - - + +
681A LEU* 4.5 13.5 - - + +
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Residues in contact with ARG 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ARG 3.1 19.2 + - - +
618A GLN* 3.7 7.6 - - + +
620A LEU* 1.3 75.7 - - - +
622A TYR* 1.3 65.3 + - - +
624A ARG* 3.4 8.7 + - - +
625A CYS* 3.0 29.4 + - - +
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Residues in contact with TYR 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 4.1 13.6 + - + +
535A LYS 4.2 6.4 + - - -
536A PRO* 3.6 42.2 - - + -
579A PHE* 4.2 14.8 - - + -
581A ASN* 4.0 18.7 - - + +
582A ILE* 3.7 34.7 + - + +
618A GLN* 3.0 14.7 + - + +
619A ALA 3.5 7.9 - - - +
620A LEU 3.3 0.2 - - - -
621A ARG* 1.3 76.0 - - - +
623A TYR* 1.3 87.9 + + - +
625A CYS* 3.2 8.5 + - + +
626A VAL* 3.1 31.2 + - + +
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Residues in contact with TYR 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 3.5 26.2 + - + -
536A PRO* 3.9 11.1 - - + +
599A PHE* 5.0 4.8 - + + -
600A ALA 5.1 0.7 - - - -
601A LEU* 3.5 50.9 - - + -
602A ASP* 3.1 28.2 + - - +
605A SER* 4.6 1.4 - - - -
606A VAL* 3.9 18.6 - - + -
619A ALA* 3.2 20.2 + - + +
620A LEU* 4.1 13.0 - - + +
621A ARG 3.4 0.2 - - - -
622A TYR* 1.3 96.7 - + - +
624A ARG* 1.3 61.7 + - - +
626A VAL* 3.2 17.5 + - + +
627A VAL* 3.3 19.1 + - + +
681A LEU* 4.3 14.8 - - + -
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Residues in contact with ARG 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A CYS* 6.3 0.6 - - - -
620A LEU 3.1 18.1 + - - +
621A ARG* 3.7 9.2 - - - +
622A TYR 3.2 0.2 - - - -
623A TYR* 1.3 77.9 - - - +
625A CYS* 1.3 57.7 + - - +
626A VAL 3.3 0.2 + - - -
627A VAL* 3.3 3.8 + - - +
628A SER* 2.9 41.0 + - - +
680A GLU 4.7 11.9 + - - +
681A LEU* 4.0 17.4 - - + +
683A ASP* 4.9 15.2 - - - +
684A LEU* 6.2 1.6 - - - +
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Residues in contact with CYS 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A CYS* 2.0 54.3 - - + +
579A PHE* 6.1 0.2 - - + -
582A ILE* 4.2 13.0 - - + +
621A ARG* 3.0 21.5 + - - +
622A TYR* 3.2 6.9 + - - +
624A ARG* 1.3 78.1 - - - +
626A VAL* 1.3 61.3 + - - +
628A SER* 3.2 7.0 - - - -
629A GLU* 3.1 29.1 + - - +
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Residues in contact with VAL 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ILE* 3.6 26.9 - - + -
597A TYR* 5.1 11.0 - - + -
599A PHE* 3.9 30.7 - - + -
622A TYR* 3.1 30.3 + - + +
623A TYR* 3.3 16.2 - - + +
624A ARG 3.1 0.4 - - - -
625A CYS* 1.3 77.5 - - - +
627A VAL* 1.3 59.7 + - - +
629A GLU* 3.4 3.9 + - - +
630A GLY* 2.9 23.0 + - - -
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Residues in contact with VAL 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A PHE* 4.1 21.3 - - + -
623A TYR 3.3 15.0 + - - +
624A ARG* 4.1 5.2 - - - +
626A VAL* 1.3 74.2 - - - +
628A SER* 1.3 56.3 + - - +
630A GLY* 3.0 2.9 + - - +
631A LEU* 2.6 44.4 + - + +
637A ALA* 4.0 23.3 - - + +
639A VAL* 4.6 2.0 - - + -
681A LEU* 5.3 6.5 - - + -
684A LEU* 3.9 26.7 - - + -
685A VAL* 4.1 22.0 - - + -
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Residues in contact with SER 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A CYS* 3.8 11.6 - - - -
624A ARG* 2.9 34.8 + - - -
625A CYS* 3.2 13.3 + - - -
627A VAL* 1.3 77.0 - - - +
629A GLU* 1.3 62.9 + - - +
631A LEU* 3.5 9.0 + - - +
632A LYS* 3.3 19.1 + - - +
684A LEU* 5.7 3.3 - - - +
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Residues in contact with GLU 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A CYS* 4.2 23.6 - - + -
577A THR* 5.1 4.7 - - - +
582A ILE* 4.7 17.7 - - + -
586A LEU* 5.7 7.2 - - + -
625A CYS 3.1 19.1 + - - +
626A VAL 3.8 3.6 - - - +
628A SER* 1.3 80.9 + - - +
630A GLY* 1.3 61.7 + - - +
632A LYS* 3.3 9.1 - - - +
633A LEU* 3.3 26.1 + - - +
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Residues in contact with GLY 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A TYR* 6.6 0.2 - - - -
626A VAL 2.9 14.8 + - - -
627A VAL* 3.0 5.6 + - - -
629A GLU* 1.3 74.1 - - - +
631A LEU* 1.3 58.8 + - - +
632A LYS 3.1 1.3 - - - -
633A LEU* 3.1 10.1 + - - +
634A GLY 2.8 23.9 + - - -
635A ILE* 3.1 26.3 + - - -
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Residues in contact with LEU 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A VAL* 2.6 39.3 + - + +
628A SER* 3.7 9.4 - - - +
629A GLU 3.4 0.2 - - - -
630A GLY* 1.3 72.9 - - - +
632A LYS* 1.3 63.1 + - - +
634A GLY* 3.4 12.6 + - - +
635A ILE 5.0 7.0 - - - +
636A SER* 5.2 10.1 - - - +
637A ALA 5.4 0.7 - - - +
684A LEU* 4.0 24.9 - - + +
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Residues in contact with LYS 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A SER 3.3 10.7 + - - +
629A GLU* 3.3 14.6 - - - +
630A GLY 3.1 0.4 - - - -
631A LEU* 1.3 81.2 - - - +
633A LEU* 1.3 62.9 + - + +
634A GLY* 3.1 4.9 + - - -
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Residues in contact with LEU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A LEU* 3.9 34.3 - - + +
589A LEU* 4.6 21.3 - - + +
590A ALA* 5.2 7.9 - - + +
629A GLU 3.3 14.1 + - - +
630A GLY* 3.1 12.9 + - - +
632A LYS* 1.3 75.3 - - + +
634A GLY* 1.3 60.7 + - - +
635A ILE* 3.4 7.8 + - + +
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Residues in contact with GLY 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A THR* 3.9 7.1 - - - +
630A GLY 2.8 5.3 + - - -
631A LEU* 3.4 11.1 + - - -
632A LYS 3.1 5.8 + - - -
633A LEU* 1.3 77.8 - - - +
635A ILE* 1.3 58.3 + - - +
636A SER* 3.3 10.8 + - - -
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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