Contacts of the helix formed by residues 663 - 675 (chain D) in PDB entry 1JFZ
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 ARG 663 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432C LYS 5.3 6.3 + - - -
433C LYS* 6.2 1.2 - - - +
435C HIS* 5.4 10.4 - - - -
437C GLU* 3.1 19.3 - - - +
438C THR* 5.7 0.2 - - - +
661D ASN* 2.7 59.2 + - - +
662D LYS* 1.3 78.1 - - - +
664D GLU* 1.3 65.3 + - - +
665D GLY* 2.9 5.7 + - - +
666D PHE 3.0 5.6 + - - +
667D LEU* 3.0 21.8 + - - +
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Residues in contact with GLU 664 (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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437C GLU* 2.7 46.9 + - + +
438C THR* 4.4 1.6 - - - -
440C GLU* 3.5 18.9 - - - +
441C PHE* 2.8 50.5 + - + +
663D ARG* 1.3 70.3 - - - +
665D GLY* 1.3 54.1 + - - +
667D LEU* 3.8 5.4 - - - +
668D SER* 2.8 42.9 + - - +
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Residues in contact with GLY 665 (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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437C GLU* 4.5 0.4 + - - -
663D ARG* 2.9 5.5 + - - +
664D GLU* 1.3 76.0 - - - +
666D PHE* 1.3 58.3 + - - -
668D SER* 4.5 0.6 - - - -
669D PRO* 2.8 27.1 - - - +
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Residues in contact with PHE 666 (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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659D SER* 2.8 30.3 - - - -
660D PRO* 4.0 24.0 - - + -
661D ASN* 3.0 43.8 - - + +
663D ARG* 3.0 3.4 + - - +
665D GLY* 1.3 74.1 - - - +
667D LEU* 1.3 60.0 + - + +
669D PRO* 2.9 22.9 - - - +
670D LEU* 3.9 31.0 + - + +
743D ILE 5.2 2.9 - - - -
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Residues in contact with LEU 667 (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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438C THR* 4.5 2.9 - - + -
441C PHE* 3.7 40.8 - - + -
655D LEU* 3.6 12.2 - - + +
656D VAL* 4.4 15.9 - - + +
659D SER* 3.3 20.2 - - - +
661D ASN 2.8 28.5 - - - +
662D LYS* 3.8 20.6 - - - +
663D ARG 3.0 19.8 + - - +
664D GLU* 3.8 4.7 - - - +
666D PHE* 1.3 77.4 - - + +
668D SER* 1.3 66.0 + - - +
670D LEU* 3.4 4.2 + - - +
671D LYS* 3.0 22.0 + - - +
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Residues in contact with SER 668 (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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441C PHE* 3.6 14.4 - - - -
664D GLU* 2.8 29.8 + - - +
665D GLY* 4.5 0.9 - - - -
667D LEU* 1.3 72.7 - - - +
669D PRO* 1.3 59.6 - - - +
671D LYS* 2.9 15.7 - - - +
672D ALA* 2.7 34.8 + - - +
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Residues in contact with PRO 669 (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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665D GLY 2.8 27.1 - - - +
666D PHE* 2.9 18.4 - - - +
668D SER* 1.3 87.0 - - - +
670D LEU* 1.3 64.2 + - + +
672D ALA* 3.1 22.3 + - + +
673D TYR* 3.2 5.7 + - - +
747D ARG* 4.7 25.6 + - + +
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Residues in contact with LEU 670 (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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655D LEU* 3.9 14.4 - - + -
666D PHE* 4.5 29.6 - - + +
667D LEU* 3.4 7.3 + - - +
668D SER 3.3 0.8 - - - -
669D PRO* 1.3 80.8 - - + +
671D LYS* 1.3 56.5 + - - +
673D TYR* 2.6 27.0 + - - +
674D LEU* 3.0 18.8 + - + +
743D ILE* 2.9 55.4 - - + +
745D GLU* 3.9 6.7 - - - +
746D GLY* 3.3 34.1 - - - +
747D ARG* 4.5 4.0 - - + +
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Residues in contact with LYS 671 (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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441C PHE* 3.5 31.0 - - + -
444C ASP* 5.8 6.0 + - - -
648D ASN* 3.2 28.1 + - - +
651D ILE* 5.4 2.2 - - + -
652D VAL* 4.3 12.9 - - + +
655D LEU* 3.7 18.0 - - + +
667D LEU 3.0 14.9 + - - +
668D SER* 2.9 18.8 - - - +
670D LEU* 1.3 75.4 - - - +
672D ALA* 1.3 63.9 + - - +
673D TYR 3.0 1.0 + - - -
674D LEU* 3.3 13.1 + - - +
675D ILE* 3.3 32.8 + - + +
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Residues in contact with ALA 672 (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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668D SER 2.7 14.9 + - - +
669D PRO* 3.2 16.8 - - + +
671D LYS* 1.3 75.6 - - - +
673D TYR* 1.3 62.4 + - - +
675D ILE* 3.9 8.8 + - - +
676D SER* 3.8 15.4 + - - -
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Residues in contact with TYR 673 (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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669D PRO 3.2 4.9 + - - +
670D LEU 2.6 17.2 + - - +
672D ALA* 1.3 68.7 - - - +
674D LEU* 1.3 67.1 + - + +
675D ILE 2.8 5.0 + - - -
676D SER* 2.7 48.3 + - - -
678D GLU* 3.8 25.5 + - - +
679D PHE* 3.5 37.0 - + + +
682D LEU* 4.1 14.0 - - - +
742D ALA* 4.4 10.5 - - + -
746D GLY* 4.3 10.5 - - - -
747D ARG* 3.3 41.7 - - - +
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Residues in contact with LEU 674 (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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651D ILE* 3.7 27.8 - - + +
655D LEU* 4.0 27.6 - - + -
670D LEU* 3.0 21.7 + - + +
671D LYS 3.3 2.2 + - - +
673D TYR* 1.3 81.9 - - + +
675D ILE* 1.3 61.2 + - - +
676D SER 3.5 0.4 - - - -
679D PHE* 3.2 34.9 - - + -
680D PHE* 4.0 4.5 - - - -
739D ILE* 3.7 32.1 - - + +
742D ALA* 3.8 27.1 - - + -
743D ILE* 4.1 11.4 - - + +
746D GLY* 5.6 0.2 - - - -
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Residues in contact with ILE 675 (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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644D ASP* 6.0 2.0 - - - +
648D ASN* 4.0 30.3 - - + +
651D ILE* 4.0 23.8 - - + -
671D LYS* 3.3 33.4 + - + +
672D ALA* 4.2 8.1 - - - +
673D TYR 2.8 1.4 + - - -
674D LEU* 1.3 81.3 - - - +
676D SER* 1.3 64.8 + - - +
680D PHE* 4.1 24.6 - - + -
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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