Contacts of the helix formed by residues 701 - 714 (chain A) in PDB entry 3NKN
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 TYR 701 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A GLN* 3.4 38.1 + - + -
671A MET* 3.5 21.2 - - + -
700A MET* 1.3 72.8 - - - +
702A PRO* 1.3 66.4 - - + +
703A ALA 4.1 3.8 - - - +
704A PHE* 3.0 5.2 + - - +
705A LYS* 2.8 25.6 + - - +
750A GLN* 2.8 24.3 + - - -
793A HIS* 2.9 28.9 + + - +
794A ARG 3.6 16.6 - - - +
795A PRO* 3.6 44.0 - - + +
1015A EDO 3.4 28.2 + - - -
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Residues in contact with PRO 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A GLN 3.2 23.6 - - - +
672A SER* 4.0 15.0 - - - +
700A MET 3.9 4.3 - - - +
701A TYR* 1.3 84.0 - - + +
703A ALA* 1.3 63.7 + - - +
705A LYS* 3.1 23.9 + - + +
706A ARG* 3.1 17.2 + - - +
1028A EDO 3.3 23.1 + - - +
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Residues in contact with ALA 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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701A TYR* 3.2 1.2 - - - +
702A PRO* 1.3 75.6 - - - +
704A PHE* 1.3 64.0 + - - +
706A ARG* 3.4 10.4 + - - +
707A VAL* 3.9 2.1 + - - +
794A ARG 3.7 3.8 - - - +
795A PRO 3.5 33.4 - - - +
796A ASP* 3.6 11.4 - - - +
797A ASN* 3.1 32.6 + - - +
1023A EDO 4.1 1.8 - - - -
1028A EDO 3.0 23.5 - - - -
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Residues in contact with PHE 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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700A MET* 3.8 26.2 - - + -
701A TYR 3.0 8.9 + - - +
703A ALA* 1.3 77.0 - - - +
705A LYS* 1.3 66.4 + - - +
707A VAL* 2.9 10.3 + - + +
708A TRP* 2.9 48.4 + + + -
763A TYR* 3.6 36.6 - + + -
791A LEU* 3.8 25.8 - - + -
792A PRO 3.3 28.7 - - - -
793A HIS* 3.6 22.9 - + + +
794A ARG 4.0 1.3 + - - +
1023A EDO 3.4 21.7 + - - +
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Residues in contact with LYS 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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672A SER* 3.4 27.4 - - - +
673A TYR 2.8 26.9 + - - +
674A GLY* 4.2 0.6 - - - -
700A MET* 3.9 19.3 - - + +
701A TYR 2.8 15.1 + - - +
702A PRO* 3.1 14.3 + - + +
704A PHE* 1.3 76.2 - - - +
706A ARG* 1.3 57.5 + - - +
708A TRP* 4.3 7.0 - - - +
709A THR* 2.8 44.7 + - - +
1012A EDO 4.0 16.2 + - - -
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Residues in contact with ARG 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A PRO 3.1 12.9 + - - +
703A ALA 3.5 7.2 - - - +
704A PHE 3.1 0.6 - - - -
705A LYS* 1.3 77.6 - - - +
707A VAL* 1.3 61.0 + - - +
709A THR* 4.6 1.8 - - - -
710A TYR* 3.5 12.3 + - - +
797A ASN* 4.2 10.0 - - - +
803A SER* 2.8 34.7 + - - -
804A SER* 4.8 3.2 + - - +
805A GLU 3.2 17.4 + - - -
807A GLU* 2.8 49.6 + - - +
810A TRP* 3.5 22.3 - - + +
811A VAL* 4.7 0.2 - - - -
1028A EDO 3.1 23.6 + - - +
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Residues in contact with VAL 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A ALA 4.1 1.8 - - - +
704A PHE* 2.9 13.8 + - + +
706A ARG* 1.3 76.5 - - - +
708A TRP* 1.3 66.2 + - - +
710A TYR* 3.2 4.7 + - - +
711A PHE* 2.9 21.1 + - - +
791A LEU* 4.2 25.4 - - + -
797A ASN* 3.9 3.1 - - - +
810A TRP* 3.8 28.0 - - + -
811A VAL* 3.7 23.9 - - + +
814A LEU* 3.9 12.3 - - + -
815A MET* 4.7 4.9 - - + -
1023A EDO 3.8 24.7 - - - -
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Residues in contact with TRP 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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675A PHE 2.9 19.6 + - - -
676A LEU* 4.2 23.1 - - + -
700A MET* 3.3 31.8 - - + +
704A PHE* 2.9 40.0 + + + +
705A LYS* 4.1 2.9 - - - +
707A VAL* 1.3 74.2 - - - +
709A THR* 1.3 59.0 + - - +
711A PHE* 3.1 32.1 + + - +
712A GLN* 2.8 56.1 + - + +
730A SER* 4.0 18.2 - - - -
763A TYR* 4.4 16.4 - - + -
764A TYR 4.5 7.4 - - - -
765A SER* 4.8 2.7 - - - -
791A LEU* 4.4 14.6 - - + -
1012A EDO 3.3 23.1 - - - -
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Residues in contact with THR 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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680A TYR* 3.6 29.7 + - + +
705A LYS* 2.8 33.2 + - - +
706A ARG* 4.6 2.0 - - - -
708A TRP* 1.3 69.8 - - - +
710A TYR* 1.3 61.4 + - - +
712A GLN* 3.2 6.4 + - - +
713A ARG* 2.8 48.8 + - + +
1012A EDO 4.2 14.0 + - - -
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Residues in contact with TYR 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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706A ARG 3.5 18.6 + - - +
707A VAL 3.2 4.8 + - - +
709A THR* 1.3 78.8 - - - +
711A PHE* 1.3 57.6 + - - +
713A ARG* 4.5 10.8 - - - +
714A VAL* 2.8 64.6 + - + +
715A LEU* 3.2 36.4 + - + +
806A ASP* 5.1 1.8 - - - -
807A GLU* 3.7 25.6 - - + -
808A SER* 3.6 35.2 + - - -
811A VAL* 3.8 21.5 - - + -
812A GLU* 4.5 12.0 + - + -
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Residues in contact with PHE 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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629A TYR* 5.0 1.3 - - - -
707A VAL* 2.9 15.0 + - + +
708A TRP* 3.4 42.4 - + + +
709A THR 3.1 0.2 - - - -
710A TYR* 1.3 77.4 - - - +
712A GLN* 1.3 79.7 + - - +
715A LEU* 3.3 19.9 + - + -
716A VAL* 3.0 47.1 + - + +
719A TYR* 4.0 17.9 - + - -
728A VAL* 5.1 1.1 - - + -
730A SER* 4.6 2.0 - - - -
765A SER* 3.4 28.9 - - - -
767A ILE* 4.1 9.6 - - + -
789A PHE* 4.9 0.2 - + - -
791A LEU* 5.5 2.5 - - + -
815A MET* 3.4 33.2 - - + -
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Residues in contact with GLN 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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629A TYR* 3.6 18.5 + - - -
675A PHE 2.7 29.7 + - - -
676A LEU 3.1 13.8 + - - +
678A PRO* 3.5 27.4 - - + +
680A TYR* 4.4 2.6 - - + +
681A LEU* 3.8 26.3 - - - +
708A TRP* 2.8 51.3 + - + +
709A THR 3.8 2.2 - - - +
711A PHE* 1.3 88.6 - - - +
713A ARG* 1.3 62.9 + - - +
716A VAL* 4.1 6.8 - - - +
717A LYS 5.0 0.3 + - - -
730A SER* 5.3 0.2 + - - -
1012A EDO 3.7 15.0 - - - +
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Residues in contact with ARG 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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637A VAL* 4.0 31.2 - - + +
680A TYR* 4.0 45.5 - - + -
681A LEU* 5.5 0.3 - - - +
709A THR* 2.8 30.4 + - - +
710A TYR* 4.5 11.5 - - - +
712A GLN* 1.3 76.0 - - - +
714A VAL* 1.3 82.4 + - + +
717A LYS* 4.5 2.3 - - - +
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Residues in contact with VAL 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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710A TYR* 2.8 52.4 + - + +
713A ARG* 1.3 113.2 - - - +
715A LEU* 1.3 67.8 + - + +
716A VAL 3.6 0.7 - - - -
717A LYS* 3.6 6.9 + - - +
718A LYS* 3.1 24.8 + - + +
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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
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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