Contacts of the helix formed by residues 709 - 730 (chain A) in PDB entry 3RFU
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 SER 709 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A TYR* 3.7 4.0 - - - -
707A LEU* 4.7 0.4 - - - +
708A LEU* 1.3 83.3 - - - +
710A PRO* 1.3 71.9 - - - +
711A MET* 3.7 9.8 + - - +
712A ILE* 2.9 52.5 + - - +
713A ALA 3.1 2.8 + - - -
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Residues in contact with PRO 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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99A GLU* 3.9 16.8 - - + +
185A ALA* 4.4 12.8 - - + -
186A VAL 3.7 23.6 - - - +
187A TYR* 3.2 39.5 - - + +
189A GLU* 4.6 9.0 - - + +
190A ALA* 6.2 1.6 - - + -
709A SER* 1.3 85.5 - - - +
711A MET* 1.3 56.2 + - - +
713A ALA* 3.5 4.4 - - + +
714A ALA* 2.7 35.3 + - - +
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Residues in contact with MET 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 5.5 10.5 - - - +
100A MET* 5.4 12.3 - - - +
102A GLY 6.2 0.2 - - - +
709A SER* 3.1 10.5 - - - +
710A PRO* 1.3 81.9 - - - +
712A ILE* 1.3 59.3 + - + +
714A ALA* 3.3 10.1 + - - +
715A ALA* 3.0 21.8 + - - +
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Residues in contact with ILE 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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380A ILE* 3.7 19.3 - - + -
692A GLY* 5.2 3.4 - - - -
695A LEU* 4.4 15.9 - - + -
708A LEU* 3.2 32.1 - - + -
709A SER* 2.9 33.3 + - - +
711A MET* 1.3 74.6 - - + +
713A ALA* 1.3 63.7 + - - +
714A ALA 3.0 1.3 - - - -
715A ALA* 2.8 24.6 + - + +
716A ALA* 3.0 12.6 + - + +
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Residues in contact with ALA 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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187A TYR* 4.8 9.9 - - + -
190A ALA* 5.0 12.1 - - + -
379A ILE* 5.5 4.7 - - + +
380A ILE* 3.9 21.0 - - + +
689A ASN* 5.7 0.2 + - - -
708A LEU* 4.9 3.1 - - + -
709A SER 3.1 6.5 + - - +
710A PRO* 3.1 14.9 + - + +
712A ILE* 1.3 87.7 - - + +
714A ALA* 1.3 57.5 + - - +
716A ALA* 3.4 4.2 + - - +
717A MET* 3.0 32.6 + - + +
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Residues in contact with ALA 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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100A MET* 4.7 14.1 - - + -
189A GLU* 3.9 21.3 - - - +
710A PRO 2.7 17.1 + - - +
711A MET* 3.4 9.9 - - - +
713A ALA* 1.3 76.4 - - - +
715A ALA* 1.3 64.2 + - - +
717A MET* 3.3 18.0 + - + +
718A ALA* 3.0 25.6 + - - +
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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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711A MET 3.0 11.0 + - - +
712A ILE* 2.8 21.6 + - + +
714A ALA* 1.3 77.6 - - - +
716A ALA* 1.3 54.2 + - - +
718A ALA* 3.5 2.8 + - - +
719A LEU* 3.0 42.1 + - + +
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Residues in contact with ALA 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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380A ILE* 4.4 11.9 - - + -
688A TYR* 4.2 12.3 - - + +
689A ASN* 3.8 35.9 - - - +
712A ILE* 3.0 11.8 + - + +
713A ALA 3.7 7.4 - - - +
714A ALA 3.3 0.2 - - - -
715A ALA* 1.3 74.9 - - - +
717A MET* 1.3 64.7 + - - +
719A LEU* 3.8 1.3 - - - +
720A SER* 3.0 30.2 + - - -
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Residues in contact with MET 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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189A GLU* 4.4 13.9 - - - +
190A ALA* 4.2 21.1 - - + -
193A VAL* 3.3 43.7 - - + -
194A ILE* 4.2 14.4 - - + -
382A CYS 5.8 2.2 - - - +
384A CYS* 3.9 18.0 - - - +
689A ASN* 5.5 3.8 - - - +
713A ALA* 3.0 20.0 + - + +
714A ALA* 3.5 23.3 - - + +
715A ALA 3.3 0.4 - - - -
716A ALA* 1.3 77.4 - - + +
718A ALA* 1.3 58.8 + - - +
720A SER* 3.9 2.0 - - - -
721A SER* 2.7 33.5 + - - -
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Residues in contact with ALA 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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714A ALA 3.0 16.1 + - - +
715A ALA* 4.0 4.3 - - - +
717A MET* 1.3 76.6 - - - +
719A LEU* 1.3 66.4 + - + +
721A SER* 3.3 5.6 + - - -
722A VAL* 3.0 30.6 + - + +
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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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688A TYR* 3.2 50.3 - - + +
715A ALA* 3.0 26.9 + - + +
716A ALA* 3.8 2.7 - - - +
718A ALA* 1.3 80.5 - - + +
720A SER* 1.3 63.2 + - - +
722A VAL* 3.4 8.1 - - + +
723A SER* 2.9 29.5 + - - +
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Residues in contact with SER 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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383A PRO* 5.7 0.4 - - - -
384A CYS* 5.1 1.1 - - - -
385A ALA* 3.6 21.8 - - - -
684A PHE 3.7 2.7 + - - -
685A ALA* 3.3 23.9 + - - +
688A TYR* 3.5 18.6 - - - +
689A ASN* 3.4 9.4 + - - -
716A ALA 3.0 18.3 + - - -
717A MET* 3.9 3.8 - - - -
719A LEU* 1.3 75.7 - - - +
721A SER* 1.3 63.5 + - - +
723A SER* 3.9 1.8 - - - -
724A VAL* 3.0 29.5 + - - +
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Residues in contact with SER 721 (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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197A LEU* 3.8 13.0 - - - +
384A CYS* 3.7 15.8 - - - -
385A ALA* 4.5 6.0 - - - +
388A LEU* 5.8 5.8 - - - -
717A MET 2.7 23.7 + - - -
718A ALA* 3.6 6.7 - - - -
720A SER* 1.3 75.0 - - - +
722A VAL* 1.3 63.8 + - - +
724A VAL* 3.1 4.7 + - - +
725A ILE* 3.0 35.2 + - - +
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Residues in contact with VAL 722 (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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718A ALA* 3.0 19.7 + - + +
719A LEU* 3.4 13.2 - - + +
721A SER* 1.3 75.9 - - - +
723A SER* 1.3 67.7 + - - +
725A ILE* 4.1 6.2 - - - +
726A ILE* 3.0 50.7 + - + +
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Residues in contact with SER 723 (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 PHE* 3.7 32.3 - - - -
688A TYR* 3.3 20.4 + - - -
719A LEU* 2.9 23.0 + - - +
720A SER 3.9 2.2 - - - -
722A VAL* 1.3 80.7 - - - +
724A VAL* 1.3 58.5 + - - +
726A ILE* 4.0 3.2 - - - +
727A ASN* 3.0 31.9 + - - +
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Residues in contact with VAL 724 (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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385A ALA* 4.3 12.8 - - + +
388A LEU* 4.5 12.6 - - + -
389A ALA* 4.1 27.8 - - + +
392A MET* 4.6 7.4 - - + -
681A ASN* 3.5 41.1 - - + +
684A PHE* 4.2 7.6 - - + -
685A ALA* 4.2 6.5 - - + +
720A SER 3.0 21.7 + - - +
721A SER* 3.1 3.1 + - - +
723A SER* 1.3 74.3 - - - +
725A ILE* 1.3 69.9 + - + +
727A ASN* 3.3 0.4 + - - -
728A ALA* 3.0 22.9 + - - +
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Residues in contact with ILE 725 (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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388A LEU* 5.2 13.0 - - + -
392A MET* 4.0 29.9 - - + +
721A SER* 3.0 22.8 + - - +
722A VAL* 4.1 5.2 - - - +
724A VAL* 1.3 76.8 - - + +
726A ILE* 1.3 66.2 + - + +
728A ALA* 3.5 1.6 + - - +
729A LEU* 3.0 47.2 + - + +
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Residues in contact with ILE 726 (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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722A VAL* 3.0 42.2 + - + +
723A SER* 4.1 4.0 - - - +
725A ILE* 1.3 78.9 - - + +
727A ASN* 1.3 58.4 + - - +
729A LEU* 3.5 11.4 + - + +
730A ARG* 3.1 24.6 + - + +
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Residues in contact with ASN 727 (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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677A ASN* 3.1 12.6 + - - -
680A GLN* 3.3 37.9 + - - +
681A ASN* 2.7 24.3 + - - +
684A PHE* 3.8 21.7 - - + -
723A SER 3.0 20.2 + - - +
725A ILE 3.3 0.2 - - - -
726A ILE* 1.3 77.5 - - - +
728A ALA* 1.3 59.3 + - - +
730A ARG* 2.9 40.3 + - - +
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Residues in contact with ALA 728 (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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392A MET* 4.0 35.9 - - + +
393A SER* 4.7 0.4 - - - -
396A VAL* 3.7 12.6 - - + +
677A ASN* 3.5 12.3 - - - +
681A ASN* 3.8 15.4 + - - +
724A VAL* 3.0 17.0 + - + +
725A ILE 4.0 3.1 - - - +
727A ASN* 1.3 72.9 - - - +
729A LEU* 1.3 58.2 + - - +
730A ARG 2.9 4.9 - - - -
731A LEU* 2.8 25.9 + - - +
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Residues in contact with LEU 729 (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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392A MET* 5.4 6.7 - - + -
396A VAL* 4.9 2.9 - - + -
725A ILE* 3.0 43.5 + - + +
726A ILE* 3.7 10.8 - - + +
728A ALA* 1.3 77.5 - - - +
730A ARG* 1.3 59.9 + - - +
732A LYS* 3.4 45.6 + - - +
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Residues in contact with ARG 730 (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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677A ASN* 4.8 1.8 - - - +
680A GLN* 5.5 1.1 - - - -
726A ILE* 3.1 15.2 + - + +
727A ASN* 2.9 32.8 - - - +
728A ALA 2.9 0.2 - - - -
729A LEU* 1.3 77.5 - - - +
731A LEU* 1.3 50.6 + - - +
732A LYS* 2.7 18.8 + - - +
733A ARG* 4.5 3.3 + - - +
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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