Contacts of the helix formed by residues 706 - 721 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635D PHE* 5.8 4.2 - - - +
636D GLN* 4.6 9.4 + - - -
639D VAL* 4.5 3.1 - - - +
704D ARG 4.8 1.0 + - - -
705D PRO* 1.3 77.0 + - - +
707D PHE* 1.3 56.6 + - - +
708D PRO* 3.1 12.3 - - - -
709D ARG* 2.5 37.9 + - - +
710D ILE* 3.0 8.7 + - - -
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Residues in contact with PHE 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D ALA* 4.3 11.2 - - + -
564D MET* 3.7 34.1 - - + -
565D ASP* 3.9 19.9 - - - +
568D HIS* 3.0 41.6 + + + +
638D ASP 4.4 0.2 - - - -
639D VAL* 3.6 27.8 - - + +
642D PHE* 3.6 53.2 - + + -
706D SER* 1.3 69.4 - - - +
708D PRO* 1.3 71.9 - - + +
710D ILE* 3.6 17.4 - - + +
711D LEU* 2.9 26.3 + - - +
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Residues in contact with PRO 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ASP* 3.8 22.0 - - - +
568D HIS* 6.1 2.5 - - + -
706D SER* 3.2 14.6 - - - -
707D PHE* 1.3 94.4 - - + +
709D ARG* 1.3 59.0 + - - +
711D LEU* 3.9 2.0 - - + +
712D ALA* 3.1 22.2 + - - +
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Residues in contact with ARG 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692D LEU* 5.2 6.0 - - - +
695D GLU* 5.6 7.3 + - - +
705D PRO* 4.5 18.3 - - + +
706D SER* 2.5 23.6 + - - +
708D PRO* 1.3 73.6 - - - +
710D ILE* 1.3 63.0 + - - +
712D ALA* 3.4 6.0 + - + +
713D GLU* 3.2 50.6 + - - +
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Residues in contact with ILE 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D ALA* 4.8 0.9 - - + -
639D VAL* 3.2 34.8 - - + -
642D PHE* 3.8 27.4 - - + -
692D LEU* 3.9 20.9 - - + +
696D CYS* 3.6 11.2 - - - -
705D PRO* 3.5 25.4 - - + -
706D SER 3.0 15.1 + - - +
707D PHE* 3.8 21.3 - - + +
709D ARG* 1.3 75.4 - - - +
711D LEU* 1.3 67.4 + - - +
713D GLU* 3.4 2.8 + - - +
714D ILE* 3.2 22.2 + - + +
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Residues in contact with LEU 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C HIS* 4.8 1.6 - - - -
478C GLY 4.6 10.5 - - - +
558D ARG* 4.1 14.4 - - + +
561D ALA* 3.8 30.4 - - + +
562D ARG* 4.1 25.1 - - + -
565D ASP* 4.1 17.7 - - + +
707D PHE 2.9 17.5 + - - +
708D PRO* 3.9 2.9 - - + +
710D ILE* 1.3 75.9 - - - +
712D ALA* 1.3 67.0 + - - +
714D ILE* 2.9 5.9 + - + -
715D GLU* 2.9 48.5 + - + +
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Residues in contact with ALA 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708D PRO 3.1 17.1 + - - +
709D ARG* 3.8 7.6 - - + +
710D ILE 3.3 0.2 - - - -
711D LEU* 1.3 79.4 - - - +
713D GLU* 1.3 62.8 + - + +
715D GLU* 3.8 7.1 + - - +
716D GLU* 3.4 26.5 + - - +
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Residues in contact with GLU 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688D ARG* 4.9 11.5 - - - +
691D ARG* 5.4 2.9 + - - -
692D LEU* 4.5 19.3 - - + -
709D ARG* 3.2 37.7 + - - +
710D ILE 3.9 3.4 - - - +
711D LEU 3.1 0.8 - - - -
712D ALA* 1.3 77.2 - - + +
714D ILE* 1.3 55.8 + - - +
716D GLU* 3.2 8.7 + - - +
717D LEU* 2.7 50.3 + - + +
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Residues in contact with ILE 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D ILE* 4.4 11.8 - - + +
557D ALA* 4.1 24.5 - - + +
558D ARG* 3.9 30.3 - - + +
561D ALA* 4.6 4.5 - - + -
642D PHE* 4.3 20.0 - - + -
646D LEU* 4.6 5.4 - - + -
689D MET* 4.8 3.8 - - + -
692D LEU* 3.6 22.7 - - + -
710D ILE* 3.2 12.8 + - + +
711D LEU* 2.9 10.4 + - + +
713D GLU* 1.3 73.2 - - - +
715D GLU* 1.3 64.4 + - - +
717D LEU* 3.5 16.6 - - + +
718D ALA* 3.1 22.5 + - - +
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Residues in contact with GLU 715 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C LYS* 3.7 14.1 + - - +
478C GLY* 5.7 0.2 - - - -
558D ARG* 3.4 31.1 + - - +
562D ARG* 2.5 36.8 + - - -
711D LEU* 2.9 35.0 + - + +
712D ALA* 3.9 7.6 - - - +
714D ILE* 1.3 77.6 - - - +
716D GLU* 1.3 60.7 + - + +
718D ALA* 3.6 3.3 - - - +
719D ARG* 3.4 42.0 + - + +
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Residues in contact with GLU 716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688D ARG* 5.7 3.6 - - - +
712D ALA 3.4 14.3 + - - +
713D GLU* 3.2 14.0 + - - +
714D ILE 3.1 0.4 - - - -
715D GLU* 1.3 75.6 - - + +
717D LEU* 1.3 67.6 + - + +
718D ALA 3.0 2.4 + - - -
719D ARG* 3.0 48.0 + - - +
720D GLU* 3.1 25.1 + - - +
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Residues in contact with LEU 717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D ILE* 5.3 3.6 - - + -
686D PRO* 5.2 10.3 - - + -
688D ARG* 3.7 37.5 - - + +
689D MET* 3.4 49.8 - - + -
692D LEU* 5.4 2.0 - - + -
713D GLU* 2.7 50.3 + - + +
714D ILE* 3.5 19.1 - - + +
716D GLU* 1.3 73.3 - - + +
718D ALA* 1.3 59.7 + - - +
720D GLU* 3.3 11.4 + - - +
721D LEU* 3.3 31.1 + - + +
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Residues in contact with ALA 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D ILE* 3.9 22.8 - - + +
558D ARG* 3.5 31.0 - - - +
714D ILE 3.1 18.4 + - - +
715D GLU* 3.6 4.3 - - - +
716D GLU 3.0 0.4 - - - -
717D LEU* 1.3 74.0 - - - +
719D ARG* 1.3 61.0 + - - +
721D LEU* 2.6 29.9 - - - +
722D SER* 3.6 4.3 - - - -
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Residues in contact with ARG 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C LYS* 6.2 2.4 - - - +
558D ARG* 5.2 2.9 - - - +
715D GLU* 3.4 29.3 + - + +
716D GLU* 3.0 39.8 + - - +
718D ALA* 1.3 76.8 - - - +
720D GLU* 1.3 63.8 + - - +
722D SER* 2.9 25.4 - - - -
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Residues in contact with GLU 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688D ARG* 2.9 41.7 + - - -
716D GLU* 3.1 21.0 + - - +
717D LEU* 3.6 14.0 - - - +
718D ALA 3.3 0.2 - - - -
719D ARG* 1.3 80.0 - - - +
721D LEU* 1.3 62.5 + - + +
722D SER 3.6 1.7 + - - -
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Residues in contact with LEU 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D MET* 4.8 11.9 - - + +
551D LYS* 5.6 11.9 - - + +
554D ILE* 4.2 25.4 - - + -
686D PRO* 3.6 31.4 - - + -
717D LEU* 3.3 17.7 + - + +
718D ALA* 2.6 18.8 - - - +
720D GLU* 1.3 79.0 - - + +
722D SER* 1.3 56.5 + - - +
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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
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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