Contacts of the helix formed by residues 701 - 720 (chain A) in PDB entry 1N0U
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 GLY 701 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662A SER* 4.5 1.6 - - - -
697A ALA 3.4 6.8 + - - -
698A ILE 4.7 2.8 + - - -
699A HIS* 3.7 2.6 - - - +
700A ARG* 1.3 81.1 - - - +
702A GLY* 1.3 66.7 + - - -
703A GLY 3.1 3.6 - - - -
704A GLN* 2.8 16.9 + - - +
705A ILE* 3.0 12.0 + - - +
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Residues in contact with GLY 702 (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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662A SER* 3.2 24.9 + - - -
701A GLY* 1.3 71.4 - - - -
703A GLY* 1.3 58.3 + - - +
704A GLN 2.8 6.1 + - - -
706A ILE* 2.8 41.5 + - - +
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Residues in contact with GLY 703 (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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580A PRO* 4.5 4.3 - - - +
701A GLY* 3.1 1.8 - - - -
702A GLY* 1.3 74.8 - - - +
704A GLN* 1.3 65.9 + - - +
706A ILE* 5.3 0.2 - - - -
707A PRO* 3.2 21.7 - - - +
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Residues in contact with GLN 704 (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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579A SER* 3.2 11.0 - - - -
580A PRO* 3.4 15.6 - - - +
581A ASN* 2.7 63.8 + - - +
584A ASN* 4.3 2.2 - - - +
698A ILE 5.6 1.3 - - - +
699A HIS* 3.8 16.2 - - - +
700A ARG* 4.6 1.6 - - - -
701A GLY* 2.8 12.3 + - - +
702A GLY 2.8 0.4 + - - -
703A GLY* 1.3 86.9 + - - +
705A ILE* 1.3 57.2 + - - +
707A PRO* 3.4 7.5 - - - +
708A THR* 2.6 27.5 + - - -
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Residues in contact with ILE 705 (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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584A ASN* 4.8 7.6 - - + -
586A ILE* 4.5 10.8 - - + -
659A ILE* 3.1 42.2 - - + -
662A SER* 3.7 22.7 - - - +
663A VAL* 4.3 15.7 - - + +
693A LEU* 4.1 13.2 - - + -
700A ARG* 3.1 34.8 - - + +
701A GLY 3.0 7.1 + - - +
704A GLN* 1.3 76.9 - - + +
706A ILE* 1.3 67.0 + - - +
708A THR* 3.0 6.9 + - - -
709A MET* 2.9 22.2 + - - +
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Residues in contact with ILE 706 (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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662A SER* 3.6 27.1 - - - +
665A ALA* 4.0 18.6 - - + -
666A ALA* 3.2 22.6 - - + +
669A TRP* 3.9 32.8 - - + -
702A GLY* 2.8 30.3 + - - +
703A GLY* 5.3 0.4 - - - -
705A ILE* 1.3 73.9 - - - +
707A PRO* 1.3 66.4 - - + +
710A ARG* 3.1 19.4 + - - +
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Residues in contact with PRO 707 (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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578A LYS 5.7 0.4 - - - -
580A PRO* 4.2 18.2 - - + -
669A TRP* 5.8 4.0 - - + -
702A GLY 3.3 9.0 - - - +
703A GLY* 3.2 22.2 - - - +
704A GLN 3.4 9.4 - - - +
706A ILE* 1.3 100.3 - - + +
708A THR* 1.3 55.1 + - - +
710A ARG* 3.8 6.9 - - + +
711A ARG* 3.0 32.0 + - - +
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Residues in contact with THR 708 (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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577A SER* 3.7 21.5 - - - +
578A LYS* 4.0 15.3 - - - -
579A SER* 2.9 20.9 - - - +
584A ASN* 4.4 6.1 - - + +
585A ARG 4.4 0.7 - - - -
586A ILE* 3.5 28.5 - - + +
704A GLN 2.6 21.5 + - - -
705A ILE* 3.0 12.4 + - - -
707A PRO* 1.3 76.4 - - - +
709A MET* 1.3 60.3 + - - +
711A ARG* 3.4 4.0 + - - +
712A ALA* 2.9 28.4 + - - +
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Residues in contact with MET 709 (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 ILE* 3.6 23.3 - - + +
588A LEU* 4.0 12.6 - - + -
646A VAL* 4.2 21.5 - - + -
663A VAL* 3.7 38.4 - - + +
666A ALA* 3.4 24.2 - - + -
667A PHE* 4.5 5.8 - - + +
686A VAL* 4.2 15.5 - - + -
688A ILE* 4.4 9.0 - - + -
705A ILE 2.9 12.3 + - - +
708A THR* 1.3 73.6 - - - +
710A ARG* 1.3 60.0 + - - +
712A ALA* 3.3 0.8 + - - -
713A THR* 2.8 52.6 + - - +
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Residues in contact with ARG 710 (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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666A ALA* 3.7 13.8 - - + +
669A TRP* 2.9 72.8 + - - +
670A ALA* 4.4 6.5 - - + -
673A GLU* 2.9 21.2 + - - -
706A ILE 3.1 17.0 + - - +
707A PRO* 3.8 6.5 - - + +
709A MET* 1.3 75.7 - - - +
711A ARG* 1.3 63.1 + - - +
713A THR* 3.4 5.7 + - - -
714A TYR* 2.4 75.2 + - + -
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Residues in contact with ARG 711 (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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577A SER* 3.5 4.9 - - - +
578A LYS 4.2 9.2 + - - -
707A PRO 3.0 19.7 + - - +
708A THR 3.7 4.0 - - - +
710A ARG* 1.3 78.1 - - - +
712A ALA* 1.3 61.4 + - - +
714A TYR* 3.4 2.9 + - - +
715A ALA* 3.1 17.7 + - - +
837A GLU 3.0 29.0 + - - -
838A TYR* 3.4 51.9 + - + +
839A TYR 3.9 3.6 + - - -
840A ASP* 2.8 40.9 + - - -
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Residues in contact with ALA 712 (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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575A ALA* 3.7 4.1 - - - +
577A SER* 3.1 20.8 + - - +
586A ILE* 4.2 19.1 - - + +
588A LEU* 3.6 28.6 - - + +
708A THR 2.9 18.1 + - - +
709A MET 3.8 1.8 - - - +
711A ARG* 1.3 74.0 - - - +
713A THR* 1.3 61.4 + - - +
715A ALA* 3.2 4.7 + - - +
716A GLY 2.8 25.6 + - - -
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Residues in contact with THR 713 (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 LEU* 4.0 10.0 - - - +
590A ALA* 5.3 1.2 - - - +
667A PHE* 4.5 11.2 - - + -
670A ALA* 3.8 24.4 - - + +
681A MET* 4.2 14.6 - - + -
684A VAL* 5.8 0.2 - - + -
686A VAL* 4.2 19.7 - - + +
709A MET* 2.8 46.1 + - - +
710A ARG 3.7 4.5 - - - -
711A ARG 3.3 0.2 - - - -
712A ALA* 1.3 75.7 - - - +
714A TYR* 1.3 57.8 + - - +
716A GLY* 3.2 1.4 + - - -
717A PHE* 2.8 29.4 + - + +
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Residues in contact with TYR 714 (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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670A ALA* 3.7 17.6 - - + -
673A GLU* 2.6 30.6 + - - +
674A GLY 4.7 0.4 - - - -
675A PRO* 3.5 33.7 - - + -
681A MET* 4.2 4.7 - - + -
710A ARG* 2.4 79.0 + - + +
711A ARG* 3.8 4.9 - - - +
713A THR* 1.3 76.1 - - - +
715A ALA* 1.3 57.3 + - - +
717A PHE* 3.5 5.0 - - - +
718A LEU* 2.9 36.1 + - - +
838A TYR* 3.7 34.5 - + + -
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Residues in contact with ALA 715 (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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575A ALA* 3.9 14.8 - - + -
576A LEU 5.2 0.2 - - - +
577A SER* 4.4 1.1 - - - +
711A ARG 3.1 14.3 + - - +
712A ALA* 3.4 9.4 - - - +
714A TYR* 1.3 74.2 - - - +
716A GLY* 1.3 65.5 + - - +
718A LEU* 3.3 2.7 + - - +
719A LEU* 2.9 31.8 + - + +
835A TRP* 3.9 11.8 - - + +
838A TYR* 3.7 27.8 - - + +
839A TYR* 4.5 5.4 - - + +
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Residues in contact with GLY 716 (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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571A SER* 2.8 28.4 + - - -
575A ALA* 3.5 16.5 - - - +
588A LEU* 4.0 10.1 - - - -
590A ALA* 3.8 5.2 - - - -
712A ALA 2.8 15.5 + - - -
713A THR 3.7 2.0 - - - -
715A ALA* 1.3 72.5 - - - +
717A PHE* 1.3 63.7 + - - +
719A LEU* 3.2 3.1 + - - +
720A ALA* 3.1 13.9 + - - +
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Residues in contact with PHE 717 (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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565A GLU* 3.6 25.8 - - + -
566A THR* 3.2 38.4 - - - -
567A VAL* 3.4 23.2 - - + +
590A ALA* 3.9 6.0 - - + +
675A PRO* 3.5 16.8 - - + -
676A ILE* 3.7 25.6 - - + -
681A MET* 3.7 23.3 - - + -
684A VAL* 3.8 12.3 - - + -
713A THR* 2.8 18.2 + - + +
714A TYR* 3.5 7.2 - - - +
716A GLY* 1.3 75.0 - - - +
718A LEU* 1.3 64.2 + - + +
720A ALA* 2.9 22.7 + - - +
722A PRO* 3.5 21.1 - - + +
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Residues in contact with LEU 718 (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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675A PRO* 3.9 18.6 - - + +
676A ILE* 4.7 6.3 - - + -
714A TYR 2.9 20.4 + - - +
717A PHE* 1.3 96.5 - - + +
719A LEU* 1.3 57.3 + - - +
721A ASP 4.1 0.2 + - - -
722A PRO* 3.3 33.1 - - + +
809A LEU* 5.0 13.0 - - + +
832A VAL* 5.4 1.3 - - + -
833A PRO 3.6 14.4 - - - +
834A GLY* 4.8 1.1 - - - -
835A TRP* 3.4 34.4 - - + +
838A TYR* 3.5 32.8 - - + -
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Residues in contact with LEU 719 (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 GLU 4.0 0.5 - - - +
571A SER* 3.8 9.9 - - - -
572A SER* 3.0 43.0 + - - +
573A GLN* 3.3 34.5 - - + +
574A THR 4.3 0.7 - - - +
575A ALA* 4.1 20.2 - - + -
715A ALA* 2.9 21.0 + - + +
716A GLY* 3.5 5.2 - - - +
718A LEU* 1.3 76.4 - - - +
720A ALA* 1.3 57.3 + - - +
721A ASP 3.4 5.5 + - - -
835A TRP* 3.2 51.8 - - + +
839A TYR* 4.9 2.9 - - + -
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Residues in contact with ALA 720 (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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567A VAL* 3.4 15.9 - - + +
568A GLU 3.3 8.0 + - - -
569A SER* 3.0 30.7 + - - +
570A GLU 3.8 5.8 - - - -
571A SER 3.8 8.7 - - - +
590A ALA* 3.9 7.0 - - + +
716A GLY 3.1 14.9 + - - +
717A PHE 2.9 9.1 + - - +
719A LEU* 1.3 76.4 - - - +
721A ASP* 1.3 72.3 + - - +
722A PRO 3.5 1.1 - - - -
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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