Contacts of the helix formed by residues 700 - 716 (chain A) in PDB entry 3K57
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 PRO 700 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695A TYR* 4.2 5.2 - - + -
698A ASN* 3.3 21.3 - - - +
699A VAL* 1.3 86.5 - - - +
701A PRO* 1.3 75.5 - - + +
702A HIS* 3.4 23.3 - - + +
703A VAL* 3.0 27.9 + - + -
704A ARG 3.0 17.7 + - - -
908P G 3.9 26.5 - - - -
813T G 4.6 2.7 - - - -
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Residues in contact with PRO 701 (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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686A LYS* 5.0 7.9 - - - +
699A VAL 3.6 0.6 - - - -
700A PRO* 1.3 85.6 - - + +
702A HIS* 1.3 62.7 + - - +
704A ARG* 3.2 10.8 + - - +
705A ALA* 3.0 19.9 + - - +
730A TYR* 4.5 12.1 - - + +
732A TRP* 3.8 27.8 - - + -
737A PRO* 3.7 21.4 - - + +
812T A 3.8 34.5 - - - +
813T G 4.2 5.6 - - - +
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Residues in contact with HIS 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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686A LYS* 3.5 22.2 + - + +
687A ARG 3.2 19.7 + - - -
688A LEU* 3.8 19.9 - - + +
700A PRO* 3.4 25.3 - - + +
701A PRO* 1.3 81.4 - - - +
703A VAL* 1.3 67.7 + - + +
705A ALA* 3.2 4.8 + - - +
706A ALA* 2.8 27.5 + - - +
728A ILE* 3.7 11.4 - - + +
730A TYR* 3.4 35.6 - - + -
908P G 4.0 2.0 - - - -
909P C 3.1 41.0 + - - -
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Residues in contact with VAL 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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688A LEU* 3.6 14.8 - - + -
692A LEU* 3.8 8.7 - - + -
695A TYR* 3.5 39.0 - - + -
699A VAL* 4.2 2.2 - - + -
700A PRO* 3.0 36.7 + - + +
702A HIS* 1.3 78.8 + - + +
704A ARG* 1.3 61.8 + - - +
706A ALA* 3.2 2.0 + - - +
707A ARG* 2.8 59.7 + - - +
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Residues in contact with ARG 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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699A VAL* 3.6 41.5 + - + +
700A PRO 3.0 5.6 + - - +
701A PRO* 3.4 12.4 - - - +
703A VAL* 1.3 76.4 - - - +
705A ALA* 1.3 59.7 + - - +
707A ARG* 3.2 7.1 + - - +
708A LEU* 2.8 40.2 + - + +
735A ASN 6.0 0.9 - - - -
736A GLY* 5.9 0.4 - - - -
737A PRO* 3.9 23.0 - - + +
813T G 3.2 27.7 + - - -
814T G 4.5 11.7 + - - -
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Residues in contact with ALA 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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701A PRO 3.0 12.8 + - - +
702A HIS 3.2 8.3 + - - +
704A ARG* 1.3 78.5 - - - +
706A ALA* 1.3 56.6 + - - +
708A LEU* 3.2 7.8 + - - +
709A ALA* 2.8 29.5 + - - +
728A ILE* 4.6 3.6 - - + -
730A TYR* 3.7 31.6 - - + -
737A PRO 4.3 10.1 + - - +
738A GLU 4.1 2.5 - - - -
739A PRO* 3.6 16.6 - - + +
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Residues in contact with ALA 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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688A LEU* 3.8 14.6 - - + -
692A LEU* 4.1 11.2 - - + -
702A HIS 2.8 16.0 + - - +
703A VAL 3.2 5.1 + - - +
705A ALA* 1.3 73.3 - - - +
707A ARG* 1.3 60.9 + - - +
709A ALA* 3.1 1.7 + - - +
710A ASP* 2.8 32.2 + - - +
722A TYR* 3.6 36.9 - - + -
728A ILE* 4.2 6.7 - - + +
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Residues in contact with ARG 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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692A LEU* 3.1 45.8 + - + +
693A SER* 4.6 5.1 + - - +
695A TYR* 3.2 26.3 + - - +
699A VAL* 3.6 30.6 - - - +
703A VAL* 2.8 32.4 + - - +
704A ARG* 3.6 7.4 - - - +
706A ALA* 1.3 77.0 - - - +
708A LEU* 1.3 62.9 + - - +
710A ASP* 4.0 2.4 - - - +
711A GLU* 3.1 38.2 + - - +
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Residues in contact with LEU 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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704A ARG* 2.8 30.1 + - + +
705A ALA 3.5 4.5 - - - +
707A ARG* 1.3 78.5 - - - +
709A ALA* 1.3 56.8 + - - +
711A GLU* 3.4 18.0 + - - +
712A GLU* 3.0 28.6 + - - +
735A ASN 6.2 0.4 - - - +
737A PRO 3.4 25.6 - - - +
738A GLU* 4.3 17.9 - - + +
739A PRO* 4.0 9.4 - - + -
742A TYR* 6.0 0.2 - - - -
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Residues in contact with ALA 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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705A ALA 2.8 20.5 + - - +
706A ALA 3.1 1.3 + - - +
708A LEU* 1.3 74.4 - - - +
710A ASP* 1.3 57.9 + - - +
712A GLU* 3.2 4.3 + - - +
713A ASN* 2.8 31.1 + - - +
721A GLN* 5.3 0.2 - - - +
722A TYR* 3.5 28.9 - - + +
739A PRO* 3.6 24.8 - - + +
741A ASP* 6.0 1.3 - - + -
742A TYR* 3.6 13.2 - - + -
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Residues in contact with ASP 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 ALA 2.8 16.1 + - - +
707A ARG* 4.4 4.0 - - - +
709A ALA* 1.3 70.8 - - - +
711A GLU* 1.3 61.2 + - - +
713A ASN* 2.7 23.5 + - - +
714A GLN* 2.9 27.1 + - - +
720A LEU* 3.2 16.9 - - + +
721A GLN* 2.6 27.0 + - - +
722A TYR* 2.8 28.6 + - - +
723A GLN* 2.5 34.1 + - - +
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Residues in contact with GLU 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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707A ARG* 3.1 30.1 + - - +
708A LEU* 3.6 18.9 - - + +
710A ASP* 1.3 76.5 - - - +
712A GLU* 1.3 62.8 + - - +
714A GLN* 3.4 21.1 + - - +
715A LYS* 3.2 31.0 + - + +
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Residues in contact with GLU 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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708A LEU 3.0 13.8 + - - +
709A ALA 3.4 8.7 - - - +
710A ASP 3.1 0.2 - - - -
711A GLU* 1.3 75.8 - - - +
713A ASN* 1.3 66.1 + - - +
715A LYS* 3.1 33.7 + - - +
716A ARG* 2.5 44.2 + - - +
742A TYR* 3.3 41.6 - - + +
744A ARG* 4.6 18.5 + - - -
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Residues in contact with ASN 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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311A TRP* 5.7 0.3 - - - -
709A ALA 2.8 18.8 + - - -
710A ASP* 2.7 33.4 + - - +
712A GLU* 1.3 76.1 - - - +
714A GLN* 1.3 63.6 + - - +
716A ARG* 3.0 9.5 + - - +
718A ARG* 3.0 44.2 + - + +
719A PRO 3.5 14.7 + - - +
720A LEU* 4.2 2.2 - - + -
721A GLN* 3.0 25.7 + - - +
722A TYR* 4.9 0.4 - - - -
742A TYR* 2.7 31.5 + - - -
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Residues in contact with GLN 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 ASP* 2.9 13.9 + - - +
711A GLU* 3.5 29.9 - - - +
712A GLU 3.3 0.2 - - - -
713A ASN* 1.3 77.0 - - - +
715A LYS* 1.3 62.7 + - + +
716A ARG 3.2 0.5 + - - -
717A GLY* 3.3 10.8 + - - +
718A ARG 4.4 4.3 - - - +
720A LEU* 4.3 18.5 - - + +
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Residues in contact with LYS 715 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711A GLU* 3.2 22.9 + - + +
712A GLU* 3.1 31.9 + - - +
714A GLN* 1.3 77.6 - - + +
716A ARG* 1.3 61.6 + - - +
717A GLY 3.6 0.2 - - - -
744A ARG* 6.1 3.0 - - - +
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Residues in contact with ARG 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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712A GLU* 2.5 40.3 + - - +
713A ASN 3.0 6.7 + - - +
715A LYS* 1.3 82.6 - - - +
717A GLY* 1.3 62.0 + - - +
718A ARG* 3.4 41.3 + - + +
742A TYR* 3.5 33.7 - - - -
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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