Contacts of the helix formed by residues 706 - 719 (chain F) in PDB entry 4MNE
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 LEU 706 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319D ASN* 6.1 5.8 - - + +
568F HIS* 5.8 0.9 - - - +
635F PHE* 3.7 34.5 - - + -
636F GLN* 3.5 42.8 - - + +
639F VAL* 4.2 4.0 - - + -
704F ARG 3.8 1.5 + - - +
705F PRO* 1.3 79.2 - - - +
707F PHE* 1.3 63.4 + - - +
708F PRO* 3.5 11.2 - - + -
709F GLN* 3.1 9.7 + - + +
710F ILE* 2.9 28.2 + - - +
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Residues in contact with PHE 707 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561F ALA* 3.7 23.8 - - + -
564F MET* 3.4 37.9 - - + +
565F ASP* 3.6 24.5 - - + -
568F HIS* 3.5 32.0 + + + +
638F ASP 4.3 2.7 - - - -
639F VAL* 3.5 26.5 - - + -
642F PHE* 3.5 48.5 - + + -
706F LEU* 1.3 73.6 - - - +
708F PRO* 1.4 71.0 - - + +
710F ILE* 3.7 9.0 - - + +
711F LEU* 2.8 28.6 + - - +
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Residues in contact with PRO 708 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F ASP* 3.4 22.4 - - - +
568F HIS* 6.4 1.8 - - + -
706F LEU* 3.6 10.5 - - + -
707F PHE* 1.4 91.0 - - + +
709F GLN* 1.3 57.0 + - - +
711F LEU* 3.4 6.8 + - + +
712F ALA* 2.8 28.5 + - - +
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Residues in contact with GLN 709 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692F LEU* 5.6 0.2 - - - -
695F GLU* 6.0 2.4 - - - +
705F PRO* 3.9 27.6 - - + +
706F LEU* 3.1 12.7 + - + +
708F PRO* 1.3 81.1 - - - +
710F ILE* 1.3 59.4 + - - +
712F ALA* 3.3 9.7 - - + +
713F SER* 3.0 33.0 + - - +
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Residues in contact with ILE 710 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561F ALA* 4.1 13.9 - - + -
639F VAL* 3.7 19.3 - - + -
642F PHE* 3.9 21.5 - - + -
692F LEU* 4.0 24.0 - - + -
696F CYS* 3.6 21.1 - - - -
705F PRO* 3.7 18.4 - - + +
706F LEU 2.9 21.9 + - - +
707F PHE* 3.3 23.8 + - + +
709F GLN* 1.3 76.8 - - - +
711F LEU* 1.3 62.4 + - - +
713F SER* 3.2 4.5 + - - -
714F ILE* 3.1 24.9 + - + +
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Residues in contact with LEU 711 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558F ARG* 3.7 36.3 - - + +
561F ALA* 4.0 11.4 - - + -
562F GLN* 3.7 34.5 - - - +
565F ASP* 3.7 28.5 - - + +
707F PHE 2.8 18.8 + - - +
708F PRO* 3.5 5.6 - - + +
710F ILE* 1.3 70.7 - - - +
712F ALA* 1.3 67.2 + - - +
714F ILE* 3.2 6.7 + - + +
715F GLU* 3.0 43.9 + - - +
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Residues in contact with ALA 712 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708F PRO 2.8 17.6 + - - +
709F GLN* 3.3 15.9 - - + +
711F LEU* 1.3 73.8 - - - +
713F SER* 1.3 62.6 + - - +
715F GLU* 3.2 10.6 + - - +
716F LEU* 3.0 27.9 + - + +
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Residues in contact with SER 713 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688F ALA* 5.6 1.7 - - - +
692F LEU* 4.0 23.3 - - - +
709F GLN* 3.0 21.0 + - - +
710F ILE 3.2 8.3 + - - -
712F ALA* 1.3 76.1 - - - +
714F ILE* 1.3 59.2 + - - +
716F LEU* 3.5 12.4 + - - +
717F LEU* 3.1 25.5 + - - +
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Residues in contact with ILE 714 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F ILE* 4.0 20.6 - - + -
557F ALA* 4.2 14.6 - - + +
558F ARG* 4.0 51.4 - - + +
561F ALA* 4.8 3.1 - - + -
642F PHE* 4.9 1.3 - - + -
689F MET* 4.8 8.3 - - - -
692F LEU* 4.0 23.1 - - + -
710F ILE* 3.1 25.5 + - + +
711F LEU* 3.2 5.4 + - - +
713F SER* 1.3 74.9 - - - +
715F GLU* 1.3 57.3 + - - +
717F LEU* 3.5 8.1 - - + +
718F ALA* 3.0 27.4 + - + +
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Residues in contact with GLU 715 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558F ARG* 5.4 11.8 - - - -
562F GLN* 5.4 3.5 + - - -
711F LEU* 3.0 41.8 + - + +
712F ALA* 3.6 8.6 - - - +
714F ILE* 1.3 77.1 - - + +
716F LEU* 1.3 64.1 + - - +
718F ALA* 3.2 9.1 + - + +
719F ARG* 3.1 35.1 + - - +
475G LYS* 5.0 12.1 + - - -
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Residues in contact with LEU 716 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712F ALA* 3.0 15.8 + - + +
713F SER* 3.7 14.1 - - - +
714F ILE 3.5 0.2 - - - -
715F GLU* 1.3 76.5 - - - +
717F LEU* 1.3 62.7 + - - +
719F ARG* 3.1 43.3 + - + +
720F SER* 3.9 2.9 + - - -
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Residues in contact with LEU 717 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F ILE* 3.5 41.3 - - + -
686F PRO* 4.2 17.3 - - + -
688F ALA* 3.6 31.0 - - + -
689F MET* 4.6 8.7 - - + -
713F SER 3.1 12.4 + - - +
714F ILE* 3.5 10.5 - - - +
716F LEU* 1.3 79.3 - - - +
718F ALA* 1.3 65.6 + - - +
719F ARG 3.2 0.9 + - - -
720F SER* 3.3 27.5 + - - +
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Residues in contact with ALA 718 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F ILE* 6.2 2.9 - - + -
558F ARG* 6.3 2.9 - - - -
714F ILE* 3.0 20.0 + - + +
715F GLU* 3.2 10.5 + - + +
717F LEU* 1.3 74.0 - - - +
719F ARG* 1.3 50.9 + - - +
720F SER 2.8 23.3 + - - +
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Residues in contact with ARG 719 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715F GLU* 3.1 25.7 + - - +
716F LEU* 3.1 34.6 + - + +
718F ALA* 1.3 71.6 - - - +
720F SER* 1.3 66.2 + - - +
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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
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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