Contacts of the helix formed by residues 706 - 722 (chain C) in PDB entry 4JVG
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 706 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635C PHE* 5.9 3.5 - - - +
636C GLN* 4.8 7.8 + - - -
639C VAL* 4.5 2.7 - - - -
704C ARG 5.2 0.7 + - - -
705C PRO* 1.3 76.0 - - - +
707C PHE* 1.3 56.1 + - - +
708C PRO* 3.2 12.3 - - - -
709C ARG* 2.6 38.6 + - - +
710C ILE* 3.0 9.5 + - - +
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Residues in contact with PHE 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C ALA* 4.5 8.5 - - + -
564C MET* 3.5 46.7 - - + -
565C ASP* 3.7 19.2 - - - +
568C HIS* 3.2 37.8 + + - +
638C ASP 4.1 9.6 - - - -
639C VAL* 4.4 7.3 - - + +
642C PHE* 3.5 54.7 - + + -
705C PRO 4.2 0.8 + - - -
706C SER* 1.3 70.9 - - - +
708C PRO* 1.3 69.7 - - + +
710C ILE* 3.5 20.8 - - + +
711C LEU* 2.8 28.1 + - - +
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Residues in contact with PRO 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C ASP* 3.4 24.6 - - - +
568C HIS* 5.9 2.2 - - + +
706C SER* 3.2 14.8 - - - -
707C PHE* 1.3 89.7 - - + +
709C ARG* 1.3 60.6 + - + +
711C LEU* 4.2 2.4 - - + +
712C ALA* 3.2 26.3 + - - +
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Residues in contact with ARG 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B VAL* 3.5 33.5 + - + +
460B GLY 2.6 36.2 + - - -
461B GLN* 4.0 3.6 - - - +
462B ARG* 4.5 10.5 - - - +
472B TYR* 4.4 19.5 - - - -
692C LEU* 5.3 2.0 - - - +
695C GLU* 5.0 10.7 + - - +
705C PRO* 4.2 21.2 - - + +
706C SER* 2.6 33.5 + - - +
708C PRO* 1.3 75.8 - - + +
710C ILE* 1.3 54.9 + - - +
712C ALA* 3.5 5.7 - - - +
713C GLU* 3.1 26.9 + - - +
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Residues in contact with ILE 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C ALA* 4.5 0.9 - - + -
639C VAL* 4.1 15.5 - - + -
642C PHE* 3.8 14.6 - - + -
692C LEU* 4.1 15.5 - - + -
696C CYS* 3.7 25.6 - - - -
705C PRO* 4.0 17.7 - - + +
706C SER 3.0 11.4 + - - +
707C PHE* 3.1 35.0 + - + +
709C ARG* 1.3 74.9 - - - +
711C LEU* 1.3 67.6 + - - +
713C GLU* 3.1 4.0 + - - +
714C ILE* 2.9 49.2 + - + +
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Residues in contact with LEU 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C ARG* 3.9 14.8 - - + +
561C ALA* 3.9 15.5 - - + +
562C ARG* 3.7 46.9 - - + +
565C ASP* 4.3 17.3 - - + +
707C PHE 2.8 18.8 + - - +
708C PRO* 4.2 2.9 - - + +
710C ILE* 1.3 72.7 - - - +
712C ALA* 1.3 54.2 + - - +
714C ILE* 3.1 4.3 + - + +
715C GLU* 2.7 46.6 + - + +
477D HIS* 4.5 3.1 - - - -
478D GLY* 4.3 21.3 - - - +
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Residues in contact with ALA 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B THR* 5.9 7.4 - - + -
459B VAL 5.8 3.4 - - - +
708C PRO 3.2 17.2 + - - +
709C ARG* 3.5 7.9 - - - +
711C LEU* 1.3 79.6 - - - +
713C GLU* 1.3 59.6 + - - +
715C GLU* 2.7 37.4 - - - +
716C GLU* 3.3 8.8 + - - +
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Residues in contact with GLU 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B GLY 5.9 0.2 - - - -
461B GLN* 4.7 15.2 + - - +
688C ARG* 3.3 30.5 - - - +
691C ARG* 3.5 13.0 + - - -
692C LEU* 3.9 29.6 - - + -
709C ARG 3.1 15.0 + - - +
710C ILE 3.1 7.8 + - - +
712C ALA* 1.3 74.3 - - - +
714C ILE* 1.3 55.0 + - - +
716C GLU* 2.5 65.1 + - - +
717C LEU* 2.9 16.7 - - + +
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Residues in contact with ILE 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554C ILE* 4.5 14.0 - - + +
557C ALA* 4.3 10.3 - - + +
558C ARG* 4.0 30.4 - - + +
561C ALA* 3.9 18.8 - - + -
642C PHE* 3.9 13.0 - - + -
646C LEU* 5.5 1.8 - - + -
689C MET* 4.8 5.8 - - + -
692C LEU* 3.5 18.8 - - + -
710C ILE* 2.9 38.7 + - + +
711C LEU* 3.7 5.6 - - + +
713C GLU* 1.3 70.9 - - - +
715C GLU* 1.3 61.6 + - - +
717C LEU* 3.4 13.4 + - + +
718C ALA* 3.2 22.5 + - - +
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Residues in contact with GLU 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A ARG* 5.4 7.5 + - - -
558C ARG* 4.5 17.1 + - - +
562C ARG* 5.4 4.5 - - - +
711C LEU* 2.7 27.8 + - + +
712C ALA* 2.7 36.8 - - - +
714C ILE* 1.3 73.7 - - - +
716C GLU* 1.3 63.2 + - - +
718C ALA* 3.5 2.8 + - - +
719C ARG* 3.3 20.8 + - - +
475D LYS* 5.1 12.3 + - - -
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Residues in contact with GLU 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B GLY* 6.1 0.3 - - - -
461B GLN* 4.2 17.5 + - - +
688C ARG* 2.6 37.1 + - - -
712C ALA 3.4 8.4 - - - +
713C GLU* 2.5 74.2 + - - +
715C GLU* 1.3 78.8 - - + +
717C LEU* 1.3 59.3 + - + +
719C ARG* 2.6 40.8 - - - +
720C GLU* 2.8 12.2 - - - +
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Residues in contact with LEU 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554C ILE* 5.2 4.5 - - + -
686C PRO* 5.3 9.6 - - + +
688C ARG* 4.0 12.3 - - + +
689C MET* 3.6 56.3 - - + +
692C LEU* 4.9 2.0 - - + -
713C GLU* 2.9 45.1 - - + +
714C ILE* 3.4 19.5 - - - +
715C GLU 3.3 0.2 - - - -
716C GLU* 1.3 81.9 - - + +
718C ALA* 1.3 64.2 + - - +
720C GLU* 3.2 24.4 - - - +
721C LEU* 3.4 13.3 + - - +
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Residues in contact with ALA 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C ILE* 4.3 17.7 - - + -
558C ARG* 2.9 34.3 - - - +
714C ILE 3.2 13.8 + - - +
715C GLU 3.7 4.7 - - - +
716C GLU 3.2 0.2 - - - -
717C LEU* 1.3 78.9 - - - +
719C ARG* 1.3 66.5 + - - +
721C LEU* 3.4 6.8 + - - +
722C SER* 2.9 25.0 + - - -
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Residues in contact with ARG 719 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A ARG* 2.4 84.3 - - - +
715C GLU 3.3 7.3 + - - +
716C GLU* 2.6 45.4 - - - +
718C ALA* 1.3 77.3 - - - +
720C GLU* 1.3 73.2 + - + +
722C SER* 3.0 24.4 - - - -
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Residues in contact with GLU 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688C ARG* 2.0 52.3 + - - -
716C GLU 2.8 18.5 - - - +
717C LEU* 3.2 9.0 - - - +
719C ARG* 1.3 87.3 - - + +
721C LEU* 1.3 60.7 + - + +
722C SER* 3.0 7.7 + - - +
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Residues in contact with LEU 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C MET* 4.8 6.7 - - + -
551C LYS* 3.1 65.3 + - + +
554C ILE* 4.4 22.9 - - + -
684C ASN 5.6 0.9 - - - +
686C PRO* 3.5 33.0 - - + -
717C LEU 3.4 12.5 + - - +
718C ALA* 3.4 7.7 + - - +
720C GLU* 1.3 75.8 - - + +
722C SER* 1.3 69.9 + - - +
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Residues in contact with SER 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C LYS* 4.8 7.6 - - - +
718C ALA 2.9 14.0 + - - -
719C ARG* 3.0 24.0 - - - -
720C GLU 3.0 4.7 - - - +
721C LEU* 1.3 86.5 - - - +
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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
------------------------------------------------------------
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