Contacts of the helix formed by residues 626 - 642 (chain A) in PDB entry 3NC0
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 GLN 626 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A GLN* 4.8 9.0 + - - +
582A ASP* 5.6 1.8 + - - +
624A ASP 5.2 2.5 - - - +
625A LEU* 1.3 75.8 - - - +
627A PRO* 1.3 79.8 - - + +
628A GLN* 3.4 5.4 - - + +
629A GLN* 2.9 38.7 + - + +
630A VAL* 3.0 21.4 + - - +
128B LYS* 5.9 0.2 - - - -
143B THR* 5.4 3.4 - - + -
145B SER* 5.2 5.3 - - - -
147B TYR* 3.2 52.0 - - + +
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Residues in contact with PRO 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU 4.7 0.9 - - - +
626A GLN* 1.3 87.0 - - + +
628A GLN* 1.3 58.7 + - + +
630A VAL* 3.1 17.3 + - + +
631A HIS* 2.6 36.6 + - + -
686A LYS* 6.1 5.4 - - - +
690A SER* 5.0 7.0 - - - +
128B LYS* 5.8 5.6 - - - -
147B TYR* 3.9 25.8 - - + +
149B VAL* 5.5 10.5 - - + -
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Residues in contact with GLN 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A VAL 4.6 6.1 - - - +
441A VAL* 3.0 34.9 - - + +
442A ARG* 3.6 26.2 + - - +
626A GLN* 3.4 3.8 - - + +
627A PRO* 1.3 80.5 - - + +
629A GLN* 1.3 64.8 + - + +
631A HIS* 3.0 24.9 + - + +
632A THR* 3.0 17.0 + - - +
693A LYS* 5.6 9.4 - - + +
697A ARG* 4.7 10.7 + - - +
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Residues in contact with GLN 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A GLN* 3.5 22.7 - - - +
582A ASP* 2.8 32.0 + - - +
585A CYS* 4.1 21.4 - - + -
625A LEU* 3.7 23.0 - - + +
626A GLN* 2.9 56.4 + - + +
628A GLN* 1.3 78.8 - - + +
630A VAL* 1.3 56.1 + - - +
632A THR* 3.1 10.8 + - - -
633A PHE* 2.9 29.1 + - - +
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Residues in contact with VAL 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A ILE* 4.1 24.5 - - + +
625A LEU* 3.9 20.4 - - + +
626A GLN 3.0 20.8 + - - +
627A PRO* 3.1 12.1 + - + +
629A GLN* 1.3 75.4 - - - +
631A HIS* 1.3 59.9 + - + +
633A PHE* 3.4 7.1 + - - +
634A TYR* 3.0 48.4 + - + -
694A THR* 5.0 8.1 - - - +
128B LYS* 5.4 6.7 - - - +
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Residues in contact with HIS 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A PRO* 2.6 36.6 + - + -
628A GLN* 3.0 16.5 + - + +
630A VAL* 1.3 75.9 - - + +
632A THR* 1.3 59.2 + - - +
634A TYR* 3.2 6.4 + - - +
635A GLU* 2.9 28.9 + - - +
690A SER* 3.3 35.3 + - - -
693A LYS* 3.4 25.5 - - + +
694A THR* 3.2 36.9 + - - +
697A ARG* 3.4 30.2 - - + +
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Residues in contact with THR 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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585A CYS* 4.6 17.9 - - + +
586A ASP* 5.0 6.1 - - - +
589A ILE* 4.0 31.7 - - + +
628A GLN* 3.0 15.9 + - - +
629A GLN* 3.5 11.3 - - - -
631A HIS* 1.3 76.5 - - - +
633A PHE* 1.3 61.3 + - - +
635A GLU* 3.6 3.5 + - - +
636A ALA* 3.2 21.5 + - - +
697A ARG* 3.8 19.1 + - - +
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Residues in contact with PHE 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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570A PHE* 3.6 24.0 - + - -
573A MET* 3.9 22.4 - - + -
585A CYS* 5.1 3.1 - - - -
588A PHE* 3.4 32.3 - + - -
614A ILE* 4.5 3.4 - - + -
618A ILE* 4.4 18.2 - - + -
621A ILE* 4.0 15.9 - - + -
622A ILE* 3.5 27.4 - - + -
625A LEU* 4.5 3.8 - - + -
629A GLN 2.9 15.7 + - - +
630A VAL* 3.6 8.7 - - - +
631A HIS 3.1 0.2 - - - -
632A THR* 1.3 76.3 - - - +
634A TYR* 1.3 74.6 + + - +
636A ALA* 3.1 14.4 + - - +
637A VAL* 3.2 29.7 + - + +
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Residues in contact with TYR 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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618A ILE* 3.7 24.2 - - + +
622A ILE* 4.0 22.1 - - + +
630A VAL* 3.0 36.0 + - + +
631A HIS 3.2 4.9 + - - +
633A PHE* 1.3 83.5 - + - +
635A GLU* 1.3 60.1 + - - +
637A VAL* 3.5 1.5 + - - -
638A GLY 3.0 7.8 + - - -
657A TYR* 2.5 71.3 + + - +
658A MET* 4.8 4.5 - - - -
660A LEU* 3.6 27.5 - - - +
661A PRO* 3.6 17.1 - - + +
694A THR* 3.7 28.9 - - + +
697A ARG* 5.4 0.4 - - + -
698A ALA* 5.1 1.1 - - + +
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Residues in contact with GLU 635 (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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589A ILE* 3.7 13.7 - - + +
631A HIS 2.9 15.4 + - - +
632A THR 3.8 5.6 - - - +
633A PHE 3.2 0.2 - - - -
634A TYR* 1.3 75.2 - - - +
636A ALA* 1.3 60.3 + - - +
638A GLY 3.2 7.6 + - - -
639A TYR* 2.9 52.2 + - + +
657A TYR* 4.4 0.4 - - - -
697A ARG* 2.7 70.2 + - + +
700A LYS* 3.6 25.0 + - + +
701A ALA* 3.5 4.9 - - + +
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Residues in contact with ALA 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PHE* 3.6 23.8 - - + -
589A ILE* 3.6 26.2 - - + +
592A ALA* 3.4 22.4 - - + +
632A THR 3.2 13.8 + - - +
633A PHE 3.1 10.6 + - - +
635A GLU* 1.3 73.8 - - - +
637A VAL* 1.3 64.6 - - - +
639A TYR* 3.3 19.1 + - - +
640A MET* 3.7 3.1 + - - +
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Residues in contact with VAL 637 (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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588A PHE* 4.4 8.3 - - + -
611A ILE* 3.6 26.9 - - + -
614A ILE* 4.1 16.8 - - + -
615A LEU* 4.0 8.5 - - + -
618A ILE* 5.5 2.7 - - + -
633A PHE* 3.2 34.8 + - + +
634A TYR* 4.0 2.0 - - - +
636A ALA* 1.3 74.1 - - - +
638A GLY* 1.3 66.3 + - - +
640A MET* 3.0 21.3 + - + +
641A ILE* 3.0 13.1 + - + +
657A TYR* 3.8 27.6 - - + -
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Residues in contact with GLY 638 (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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634A TYR 3.0 10.1 + - - -
635A GLU 3.2 5.4 + - - -
636A ALA 3.2 0.8 - - - -
637A VAL* 1.3 77.2 - - - +
639A TYR* 1.3 56.4 + - - +
641A ILE* 3.2 5.9 + - - +
642A GLY* 3.0 22.5 + - - -
657A TYR* 3.2 24.6 + - - -
701A ALA* 3.6 13.0 - - - -
702A VAL* 3.7 15.6 + - - +
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Residues in contact with TYR 639 (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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589A ILE* 4.0 11.6 - - + +
592A ALA 4.5 2.2 - - - +
593A GLN* 3.4 54.4 + - + +
596A ARG* 3.6 42.9 + - - +
635A GLU* 2.9 54.5 + - + +
636A ALA* 3.3 12.8 + - - +
637A VAL 3.1 0.8 - - - -
638A GLY* 1.3 73.5 - - - +
640A MET* 1.3 65.5 + - - +
642A GLY* 3.2 10.4 + - - +
643A ALA 3.5 6.6 + - - -
700A LYS* 4.5 13.4 - - - +
701A ALA* 3.4 26.0 - - + -
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Residues in contact with MET 640 (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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588A PHE* 4.6 7.4 - - - -
592A ALA* 4.5 9.4 - - + -
596A ARG* 4.1 11.0 - - - +
599A PHE* 3.3 51.8 - - + -
600A VAL* 2.9 25.9 - - + +
611A ILE* 3.3 33.0 - - + -
614A ILE* 3.6 27.8 - - + -
636A ALA 3.7 5.3 + - - +
637A VAL* 3.0 23.6 + - + +
639A TYR* 1.3 78.5 - - - +
641A ILE* 1.3 63.1 + - - +
643A ALA* 2.9 11.3 + - - +
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Residues in contact with ILE 641 (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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600A VAL* 4.8 2.5 - - + -
611A ILE* 4.1 24.9 - - + -
615A LEU* 4.5 0.9 - - + -
637A VAL* 3.0 22.5 + - + +
638A GLY* 3.2 10.7 + - - +
640A MET* 1.3 76.0 - - - +
642A GLY* 1.3 58.0 + - - +
643A ALA 3.0 4.4 + - - -
644A GLN* 3.3 9.5 + - - +
650A GLN* 2.8 32.2 + - + +
653A LEU* 3.8 35.0 - - + +
654A ILE* 3.6 31.2 - - + -
657A TYR* 4.2 14.8 - - + -
702A VAL* 4.3 9.6 - - + -
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Residues in contact with GLY 642 (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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596A ARG* 5.0 8.1 + - - -
638A GLY 3.0 13.1 + - - -
639A TYR 3.2 7.3 + - - -
640A MET 3.1 1.2 - - - -
641A ILE* 1.3 74.7 - - - +
643A ALA* 1.3 58.7 + - - +
644A GLN 3.5 1.1 - - - -
645A THR* 4.9 5.4 - - - +
650A GLN* 3.6 13.2 + - - -
701A ALA 4.6 4.0 - - - -
702A VAL* 4.2 16.6 - - - -
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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
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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