Contacts of the helix formed by residues 705 - 727 (chain E) in PDB entry 1NLW
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 ALA 705 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706E HIS* 1.3 64.5 + - - +
707E HIS* 4.0 11.0 - - + +
708E ASN* 3.4 43.7 + - - +
709E ALA* 3.5 7.6 + - - +
812J T 5.3 2.2 + - - +
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Residues in contact with HIS 706 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705E ALA* 1.3 71.3 - - - +
707E HIS* 1.3 60.5 + - - +
709E ALA* 3.1 12.3 + - + +
710E LEU* 2.9 52.2 + - + +
605H T 3.1 40.4 + - - -
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Residues in contact with HIS 707 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705E ALA* 4.0 8.3 - - + +
706E HIS* 1.3 80.9 + - - +
708E ASN* 1.3 57.4 + - - +
710E LEU* 3.3 13.8 + - + +
711E GLU* 2.9 35.2 + - + +
605H T 6.2 5.2 - + + -
606H A 4.6 14.5 + + - -
607H G 3.3 18.6 + - - -
608H C 4.4 3.4 + - - -
812J T 3.8 17.6 - - + +
813J G 2.9 45.7 + + - -
814J C 3.8 6.4 + - - -
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Residues in contact with ASN 708 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705E ALA* 3.4 32.0 + - - +
706E HIS 3.2 0.4 - - - -
707E HIS* 1.3 80.8 + - - +
709E ALA* 1.3 62.4 + - - +
711E GLU* 3.5 2.4 + - - +
712E ARG* 3.0 23.1 + - - +
715E ARG* 4.7 2.4 + - - -
811J G 3.5 43.2 + - + +
812J T 2.7 47.2 + - - +
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Residues in contact with ALA 709 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705E ALA 3.5 7.7 + - - +
706E HIS* 3.1 17.7 + - + +
708E ASN* 1.3 79.5 - - - +
710E LEU* 1.3 62.8 + - - +
712E ARG* 3.1 8.9 + - - +
713E LYS* 3.0 45.6 + - - +
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Residues in contact with LEU 710 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706E HIS* 2.9 50.1 + - + +
707E HIS* 3.7 16.2 - - + +
709E ALA* 1.3 75.5 - - - +
711E GLU* 1.3 63.3 + - - +
713E LYS* 3.0 10.6 + - + +
714E ARG* 2.9 22.1 + - - +
605H T 4.0 28.3 - - + +
606H A 3.5 28.3 - - + +
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Residues in contact with GLU 711 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707E HIS* 2.9 26.3 + - - +
708E ASN 3.8 3.8 - - - +
710E LEU* 1.3 73.0 - - - +
712E ARG* 1.3 56.5 + - - +
714E ARG* 2.6 47.7 + - - +
715E ARG* 2.9 48.2 + - - +
607H G 4.2 3.8 - - - +
608H C 3.0 27.7 + - - -
609H A 3.5 11.3 + - - -
811J G 4.5 0.2 - - - +
812J T 3.3 26.5 - - + +
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Residues in contact with ARG 712 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ARG* 3.0 46.1 - - - +
708E ASN 3.0 13.8 + - - +
709E ALA* 3.2 12.6 - - - +
710E LEU 3.1 0.2 - - - -
711E GLU* 1.3 76.7 - - - +
713E LYS* 1.3 58.3 + - + +
715E ARG* 3.1 25.8 + - - +
716E ASP* 2.9 32.8 + - - +
810J C 3.0 35.0 + - - +
811J G 4.3 12.3 - - - +
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Residues in contact with LYS 713 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASP* 3.3 29.7 + - - +
269B ARG* 2.9 37.2 - - - +
709E ALA* 3.0 43.7 + - - +
710E LEU* 3.0 13.0 + - + +
712E ARG* 1.3 78.5 - - - +
714E ARG* 1.3 62.0 + - - +
716E ASP* 3.2 11.3 + - - +
717E HIS* 2.9 40.7 + - + +
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Residues in contact with ARG 714 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539D THR* 5.4 1.2 - - - -
540D LEU* 5.9 2.0 - - + +
710E LEU 2.9 11.9 + - - +
711E GLU* 2.6 51.1 + - - +
713E LYS* 1.3 77.8 - - - +
715E ARG* 1.3 73.0 + - - +
717E HIS* 3.3 13.1 + - - +
718E ILE* 3.2 46.9 + - + +
606H A 5.2 3.8 - - + -
607H G 3.9 40.2 + - - +
608H C 3.5 42.8 + - - +
609H A 5.0 1.2 + - - +
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Residues in contact with ARG 715 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708E ASN 4.7 1.0 + - - -
711E GLU* 2.9 29.5 + - - +
712E ARG* 3.1 25.6 + - - +
714E ARG* 1.3 93.1 - - - +
716E ASP* 1.3 56.5 + - - +
718E ILE* 3.1 10.8 + - + +
719E LYS* 2.8 30.4 + - - +
739E ARG* 4.8 2.9 + - - +
809J A 4.5 8.3 - - + -
810J C 2.4 79.8 + - - +
811J G 3.4 29.2 + - - -
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Residues in contact with ASP 716 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLN* 5.7 5.4 - - + +
265B ASP* 5.5 4.8 - - - +
266B ASP* 4.8 1.4 - - - +
269B ARG* 3.1 27.5 + - - -
712E ARG* 2.9 19.9 + - - +
713E LYS* 3.2 15.2 + - - +
715E ARG* 1.3 75.2 - - - +
717E HIS* 1.3 58.5 + - + +
719E LYS* 3.1 17.6 + - - +
720E ASP* 2.8 29.7 + - - +
810J C 4.6 12.1 + - - -
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Residues in contact with HIS 717 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B HIS* 4.6 4.8 + - - -
262B GLN* 2.9 36.5 + - - +
540D LEU* 4.3 21.1 - - + -
713E LYS* 2.9 39.4 + - + +
714E ARG* 3.6 10.1 - - - +
715E ARG 3.2 0.2 - - - -
716E ASP* 1.3 77.1 - - + +
718E ILE* 1.3 58.4 + - - +
720E ASP* 3.3 8.4 + - - +
721E SER* 2.9 32.6 + - - -
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Residues in contact with ILE 718 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539D THR* 4.1 23.6 - - + -
540D LEU* 4.4 19.3 - - + +
543D LEU* 4.1 5.2 - - + -
714E ARG* 3.2 49.5 + - + +
715E ARG* 3.1 11.7 + - + +
717E HIS* 1.3 76.0 - - + +
719E LYS* 1.3 67.3 + - - +
721E SER* 3.2 7.2 + - - -
722E PHE* 3.0 47.3 + - + -
739E ARG* 4.1 12.1 - - - +
608H C 5.2 0.7 - - - +
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Residues in contact with LYS 719 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715E ARG 2.8 13.0 + - - +
716E ASP* 3.3 18.9 + - - +
718E ILE* 1.3 75.7 - - - +
720E ASP* 1.3 64.2 + - - +
722E PHE* 3.2 6.1 + - - +
723E HIS* 3.2 49.9 + - + +
739E ARG* 3.7 17.5 - - - +
809J A 3.5 32.4 + - - +
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Residues in contact with ASP 720 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B HIS* 2.6 40.8 + - + -
716E ASP 2.8 12.8 + - - +
717E HIS* 3.3 13.7 - - - +
719E LYS* 1.3 77.8 - - - +
721E SER* 1.3 58.8 + - - +
723E HIS* 3.3 9.4 + - - +
724E SER* 3.0 36.1 + - - -
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Residues in contact with SER 721 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D LEU* 3.1 19.7 - - - +
543D LEU* 3.7 29.8 - - - +
544D THR* 4.3 8.0 + - - -
717E HIS 2.9 15.0 + - - -
718E ILE 3.2 7.2 + - - -
720E ASP* 1.3 77.4 + - - +
722E PHE* 1.3 67.1 + - - +
724E SER* 3.1 7.1 + - - +
725E LEU* 2.9 24.8 + - - +
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Residues in contact with PHE 722 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D LEU* 5.9 2.5 - - + -
521D LEU* 5.7 2.5 - - + -
539D THR* 4.8 6.3 - - + -
543D LEU* 3.5 26.7 - - + +
718E ILE* 3.0 37.1 + - + -
719E LYS* 3.2 9.4 + - - +
721E SER* 1.3 76.4 - - - +
723E HIS* 1.3 63.9 + - + +
725E LEU* 3.2 6.2 + - - +
726E ARG* 2.9 28.2 + - - +
739E ARG* 3.6 62.1 - - + +
742E ILE* 3.6 24.1 - - + +
743E LEU* 3.9 31.2 - - + -
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Residues in contact with HIS 723 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719E LYS* 3.2 44.1 + - + +
720E ASP* 3.6 10.3 - - - +
721E SER 3.1 0.6 - - - -
722E PHE* 1.3 82.9 - - + +
724E SER* 1.3 59.3 + - - +
726E ARG* 3.7 35.5 + - - +
727E ASP* 2.9 38.3 + - - +
742E ILE* 5.0 5.4 - - + -
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Residues in contact with SER 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D LYS* 3.7 40.0 + - - +
720E ASP* 3.0 27.4 + - - -
721E SER* 3.1 7.8 + - - -
723E HIS* 1.3 77.0 - - - +
725E LEU* 1.3 62.4 + - - +
727E ASP* 3.9 6.3 + - - +
728E SER* 3.7 14.0 + - - -
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Residues in contact with LEU 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D LEU* 4.3 13.9 - - + -
543D LEU* 3.9 37.7 - - + +
546D ALA* 4.4 4.5 - - + -
547D LYS* 4.1 16.6 - - + +
550D ILE* 3.8 27.1 - - + -
721E SER 2.9 12.4 + - - +
722E PHE* 3.5 9.4 - - - +
724E SER* 1.3 76.1 - - - +
726E ARG* 1.3 65.4 + - - +
728E SER* 3.0 22.5 + - - +
729E VAL* 3.4 7.3 - - - +
742E ILE* 3.9 18.4 - - + -
743E LEU* 4.6 2.5 - - + -
746E ALA* 4.0 17.9 - - + -
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Residues in contact with ARG 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722E PHE 2.9 8.9 + - - +
723E HIS* 3.7 41.1 + - - +
725E LEU* 1.3 77.1 - - - +
727E ASP* 1.3 80.6 + - - +
728E SER 3.0 5.2 + - - -
729E VAL* 3.2 11.1 + - - +
732E LEU* 3.6 28.4 - - + +
733E GLN 3.3 15.8 + - - -
734E GLY 5.1 2.2 + - - -
735E GLU 3.5 25.7 + - - -
736E LYS* 4.3 13.1 - - - +
737E ALA* 4.4 13.4 + - + +
742E ILE* 3.4 37.9 - - + +
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Residues in contact with ASP 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D LYS* 5.3 1.2 + - - -
723E HIS* 2.9 23.8 + - - +
724E SER* 3.9 7.0 + - - +
725E LEU 3.2 0.4 - - - -
726E ARG* 1.3 99.5 + - - +
728E SER* 1.3 56.7 + - - +
729E VAL 3.5 0.4 - - - -
733E GLN* 3.2 32.1 - - + +
734E GLY* 3.7 18.2 + - - -
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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
------------------------------------------------------------
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