Contacts of the helix formed by residues 688 - 698 (chain A) in PDB entry 1NU6
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 688 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A TYR* 4.0 16.2 - - + -
637A SER* 3.8 30.1 - - - +
638A MET* 4.0 12.6 - - + -
656A VAL 4.3 1.3 - - - +
657A SER* 2.9 27.9 + - - +
687A THR* 1.3 71.8 - - - +
689A MET* 1.3 67.6 + - - +
691A ARG* 3.0 19.5 + - - +
692A ALA* 3.8 2.6 + - - -
695A PHE* 4.0 18.9 - - + -
719A ILE* 3.8 33.2 - - + -
723A LEU* 6.4 0.2 - - + -
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Residues in contact with MET 689 (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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657A SER* 3.6 36.6 - - - +
658A ARG* 3.9 24.0 - - + -
661A TYR* 4.2 2.0 - - + -
687A THR* 3.2 3.0 - - - +
688A VAL* 1.3 77.7 - - - +
690A SER* 1.3 61.9 + - - +
691A ARG 3.0 1.4 + - - -
692A ALA* 3.1 20.8 + - - +
718A GLN* 3.3 29.8 - - + +
719A ILE* 3.8 20.0 - - - +
722A ALA* 3.5 18.2 - - + +
244B GLU* 3.2 46.7 - - + +
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Residues in contact with SER 690 (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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684A ARG 5.1 4.9 - - - -
685A ASN* 4.4 13.1 + - - -
687A THR* 3.1 29.6 + - - -
688A VAL 3.1 0.2 + - - -
689A MET* 1.3 76.0 - - - +
691A ARG* 1.3 65.1 + - - +
692A ALA 3.3 2.1 + - - -
693A GLU* 5.2 1.9 + - - +
244B GLU* 4.9 1.7 + - - -
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Residues in contact with ARG 691 (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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599A GLY 4.0 9.9 + - - -
600A THR* 6.2 0.2 - - - +
603A VAL* 4.5 6.5 - - - +
637A SER 5.4 0.4 - - - +
638A MET* 2.9 71.1 + - - +
641A GLY* 3.3 23.6 - - - +
642A SER* 3.9 15.9 - - - +
685A ASN* 5.0 7.9 + - - -
687A THR 4.3 2.1 + - - +
688A VAL* 3.0 9.8 + - - +
690A SER* 1.3 87.8 + - - +
692A ALA* 1.3 63.5 + - - +
693A GLU* 3.3 2.9 - - - -
694A ASN* 3.0 26.7 + - - +
695A PHE* 3.5 9.5 - - + -
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Residues in contact with ALA 692 (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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688A VAL 3.8 2.7 + - - -
689A MET* 3.1 16.2 + - - +
690A SER 3.3 2.4 + - - -
691A ARG* 1.3 76.1 - - - +
693A GLU* 1.3 62.4 + - - +
695A PHE* 2.9 29.6 + - - +
722A ALA* 3.7 31.6 - - + +
723A LEU* 3.8 8.1 - - + +
726A VAL* 4.2 14.4 - - + -
728A VAL* 3.6 8.1 - - - +
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Residues in contact with GLU 693 (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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690A SER 5.2 0.2 + - - -
691A ARG 3.1 1.5 + - - +
692A ALA* 1.3 78.3 - - - +
694A ASN* 1.3 63.6 + - - +
695A PHE 3.3 0.5 + - - -
696A LYS* 3.0 55.5 + - - +
726A VAL* 3.3 44.3 - - + +
728A VAL* 4.4 0.5 - - - +
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Residues in contact with ASN 694 (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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640A LEU 4.3 6.6 - - - +
641A GLY* 2.6 36.2 + - - +
642A SER* 4.0 8.7 + - - +
643A GLY* 4.2 13.6 - - - +
691A ARG* 3.0 16.4 + - - +
693A GLU* 1.3 79.7 - - - +
695A PHE* 1.3 56.2 + - - +
696A LYS* 2.9 14.0 + - - +
697A GLN* 3.2 33.0 + - - +
698A VAL 4.7 0.3 + - - -
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Residues in contact with PHE 695 (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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637A SER* 3.2 23.8 - - - -
640A LEU* 4.0 15.0 - - + -
641A GLY* 3.7 17.9 - - - -
688A VAL* 4.0 24.9 - - + -
691A ARG* 3.5 20.2 - - + -
692A ALA* 2.9 15.2 + - - +
694A ASN* 1.3 74.8 - - - +
696A LYS* 1.3 59.6 + - - +
697A GLN 3.0 3.5 + - - -
698A VAL* 3.1 28.0 + - + +
700A TYR* 3.5 55.6 - + + +
723A LEU* 3.7 13.0 - - + -
728A VAL* 3.6 22.0 - - + +
729A ASP 5.0 0.3 - - - +
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Residues in contact with LYS 696 (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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693A GLU* 3.0 40.8 + - - +
694A ASN* 2.9 5.2 + - - +
695A PHE* 1.3 78.4 - - - +
697A GLN* 1.3 75.6 + - + +
698A VAL 3.3 2.5 + - - +
727A GLY 5.9 0.7 - - - +
728A VAL* 3.9 18.4 - - + +
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Residues in contact with GLN 697 (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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640A LEU 5.8 0.2 - - - +
643A GLY* 3.9 33.6 + - - +
645A GLY* 4.4 12.3 + - - -
647A PHE 4.8 2.4 - - - +
648A LYS* 5.0 1.4 - - - +
694A ASN* 3.2 27.2 + - - +
695A PHE 3.0 1.4 - - - -
696A LYS* 1.3 93.8 - - + +
698A VAL* 1.3 67.2 + - + +
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Residues in contact with VAL 698 (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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640A LEU* 4.0 45.3 - - + +
645A GLY* 6.4 1.1 - - - -
647A PHE* 3.6 19.7 - - + +
648A LYS 3.7 13.5 - - - +
695A PHE* 3.1 32.7 - - + +
696A LYS 3.3 2.3 - - - +
697A GLN* 1.3 93.7 - - + +
699A GLU* 1.3 73.1 + - - +
700A TYR* 4.1 2.6 + - + +
729A ASP 4.9 6.2 - - - +
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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