Contacts of the helix formed by residues 686 - 697 (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 PRO 686 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550D MET* 4.5 12.1 - - + -
554D ILE* 4.7 8.5 - - + -
684D ASN 3.3 10.5 - - - +
685D CYS* 1.3 93.0 - - - +
687D LYS* 1.3 65.8 + - - +
688D ARG* 4.6 2.7 - - + +
689D MET* 3.1 29.4 - - + +
690D LYS* 3.1 6.6 + - - +
717D LEU* 5.2 9.9 - - + -
721D LEU* 3.6 35.0 - - + -
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Residues in contact with LYS 687 (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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685D CYS 3.5 3.5 + - - +
686D PRO* 1.3 66.6 - - - +
688D ARG* 1.3 66.6 + - + +
689D MET 2.9 5.6 + - - -
690D LYS* 2.9 17.3 + - - +
691D ARG* 2.9 27.0 + - + +
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Residues in contact with ARG 688 (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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686D PRO* 3.4 2.8 - - + +
687D LYS* 1.3 78.9 - - + +
689D MET* 1.3 56.0 + - - +
691D ARG* 3.4 31.7 + - - +
692D LEU* 3.1 25.8 + - - +
713D GLU* 4.9 10.0 - - - +
716D GLU* 5.7 4.4 - - - +
717D LEU* 3.7 30.2 - - + +
720D GLU* 2.9 40.9 + - - -
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Residues in contact with MET 689 (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* 3.6 22.7 - - + -
557D ALA* 5.2 2.5 - - + -
646D LEU* 4.4 20.9 - - - -
650D MET* 3.3 31.4 - - + -
685D CYS* 3.2 26.0 - - - -
686D PRO* 3.1 18.7 + - + +
687D LYS 2.9 0.4 - - - -
688D ARG* 1.3 75.6 - - - +
690D LYS* 1.3 58.4 + - - +
691D ARG 3.1 2.0 - - - -
692D LEU* 3.1 7.1 + - - +
693D MET* 2.9 28.9 + - + +
714D ILE* 4.8 11.7 - - + -
717D LEU* 3.4 32.1 - - + +
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Residues in contact with LYS 690 (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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678D LEU* 3.7 37.7 + - + +
679D SER* 4.6 5.1 - - - +
681D VAL* 3.4 38.0 - - + +
685D CYS* 4.5 12.3 - - + +
686D PRO 3.1 7.7 + - - +
687D LYS* 2.9 10.4 + - - +
689D MET* 1.3 81.1 - - - +
691D ARG* 1.3 62.6 + - + +
693D MET* 3.5 9.8 - - - +
694D ALA* 3.2 21.5 + - - +
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Residues in contact with ARG 691 (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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687D LYS* 2.9 22.1 + - + +
688D ARG* 3.4 41.1 + - - +
690D LYS* 1.3 76.7 - - + +
692D LEU* 1.3 65.5 + - - +
694D ALA* 3.0 8.8 + - - +
695D GLU* 2.8 36.7 + - + +
713D GLU* 5.4 3.8 + - - -
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Residues in contact with LEU 692 (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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646D LEU* 4.3 10.1 - - + -
688D ARG 3.1 13.3 + - - +
689D MET* 3.1 12.9 + - - +
691D ARG* 1.3 78.2 - - - +
693D MET* 1.3 65.4 + - - +
695D GLU* 2.8 21.4 + - + +
696D CYS* 3.0 20.0 + - - -
705D PRO* 4.7 9.9 - - + -
709D ARG* 5.2 4.7 - - - +
710D ILE* 3.9 38.8 - - + +
713D GLU* 4.5 19.5 - - + -
714D ILE* 3.6 33.4 - - + -
717D LEU* 5.4 2.7 - - + -
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Residues in contact with MET 693 (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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643D GLY* 4.2 8.7 - - - +
646D LEU* 3.5 27.8 - - + +
647D TYR* 3.4 45.1 - - - +
650D MET* 3.5 25.6 - - + -
678D LEU* 4.5 9.6 - - + -
681D VAL* 4.2 13.5 - - + -
685D CYS* 5.2 0.2 - - - -
689D MET* 2.9 14.3 + - + +
690D LYS* 3.5 14.4 - - - +
692D LEU* 1.3 74.5 - - - +
694D ALA* 1.3 55.7 + - - +
696D CYS* 2.8 26.9 + - - +
697D LEU* 3.1 28.8 + - + +
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Residues in contact with ALA 694 (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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678D LEU* 3.7 19.5 - - + -
690D LYS 3.2 10.4 + - - +
691D ARG* 3.0 11.2 + - - +
693D MET* 1.3 80.2 - - - +
695D GLU* 1.3 61.0 + - - +
697D LEU* 3.6 13.1 + - - +
698D LYS* 3.3 33.5 + - - +
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Residues in contact with GLU 695 (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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691D ARG* 2.8 38.2 + - + +
692D LEU* 2.8 16.3 + - + +
694D ALA* 1.3 78.3 - - - +
696D CYS* 1.3 61.0 + - - +
698D LYS* 3.3 33.0 + - - +
703D GLU 3.8 9.9 - - - +
704D ARG* 3.3 6.1 - - - -
705D PRO* 3.0 29.3 - - + +
709D ARG* 5.6 6.8 + - - +
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Residues in contact with CYS 696 (chain D).
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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639D VAL* 3.6 21.5 - - + +
640D TYR* 3.6 7.7 - - - -
642D PHE* 4.6 1.6 - - - -
643D GLY* 3.7 15.7 - - - -
646D LEU* 4.4 9.4 - - - -
692D LEU* 3.1 21.8 - - - -
693D MET* 2.8 11.0 + - - +
695D GLU* 1.3 77.7 - - - +
697D LEU* 1.3 56.9 + - - +
698D LYS 3.2 2.0 - - - -
704D ARG* 3.0 28.5 - - - +
705D PRO* 3.9 8.5 - - - -
710D ILE* 3.6 29.2 - - - -
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Residues in contact with LEU 697 (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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640D TYR* 3.8 26.9 - - + +
643D GLY* 3.2 42.6 - - - +
644D ILE* 3.5 11.9 - - + +
647D TYR* 5.2 2.9 - - + -
675D SER* 4.3 13.7 + - - +
676D PRO* 4.3 18.8 - - + -
678D LEU* 4.2 20.2 - - + -
693D MET* 3.1 33.0 + - + +
694D ALA* 3.6 6.9 + - - +
695D GLU 3.4 0.4 - - - -
696D CYS* 1.3 73.0 - - - +
698D LYS* 1.3 66.9 + - - +
699D LYS* 3.2 10.4 + - - +
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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