Contacts of the helix formed by residues 650 - 670 (chain D) in PDB entry 4PQP
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 TYR 650 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624C GLU* 5.7 4.8 - - + +
625C SER* 5.2 12.8 - - - -
628C THR* 4.5 27.3 - - - +
633C ALA* 5.8 0.7 - - - +
638C GLN* 5.6 1.7 + - - -
572D VAL* 3.6 40.0 + - + -
574D PHE* 3.7 38.5 - + + -
587D PRO* 4.5 10.3 - - + +
649D ASN* 1.3 71.8 + - - +
651D GLU* 1.3 83.3 + - + +
653D LEU* 3.1 6.3 + - - +
654D LYS* 2.9 57.7 + - + +
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Residues in contact with GLU 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ARG* 4.2 15.8 + - - +
644A ILE 4.3 12.3 - - - +
645A ILE* 4.6 10.3 - - + -
646A GLY 4.8 12.6 - - - +
625C SER* 4.8 10.9 + - - -
649D ASN* 2.7 15.0 + - - +
650D TYR* 1.3 93.0 - - + +
652D PHE* 1.3 60.3 + - - +
654D LYS* 3.3 21.2 + - - +
655D SER* 3.1 21.1 + - - -
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Residues in contact with PHE 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ARG* 2.9 44.5 - - - +
652A PHE* 4.3 12.1 - + - -
655A SER* 5.6 3.4 - - - -
656A LYS* 5.8 2.7 - - - -
617D TYR* 3.8 34.3 - + - -
649D ASN* 3.1 25.6 + - - +
650D TYR 3.1 0.6 - - - -
651D GLU* 1.3 75.3 - - - +
653D LEU* 1.3 77.1 + - + +
655D SER* 2.8 20.3 + - - -
656D LYS* 3.2 41.2 + - + +
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Residues in contact with LEU 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D VAL* 4.0 11.2 - - + -
587D PRO* 3.6 40.2 - - + +
588D VAL* 4.2 3.6 - - - +
589D PHE* 3.2 48.2 - - + -
617D TYR* 4.2 27.1 - - + +
649D ASN 3.3 20.6 + - - +
650D TYR* 3.1 8.4 + - - +
652D PHE* 1.3 86.9 - - + +
654D LYS* 1.3 64.8 + - - +
656D LYS* 3.2 11.7 + - - +
657D ARG* 3.2 10.0 + - - +
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Residues in contact with LYS 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C GLN* 6.1 0.6 - - - +
570D PRO 5.5 0.2 + - - -
571D TYR* 4.8 4.9 - - - +
572D VAL* 3.4 36.2 + - + +
650D TYR* 2.9 53.2 + - + +
651D GLU* 3.3 21.8 - - - +
653D LEU* 1.3 77.0 - - - +
655D SER* 1.3 58.0 + - - +
657D ARG* 3.2 38.2 + - - +
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Residues in contact with SER 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ARG* 3.2 30.2 + - - -
644A ILE 6.0 0.4 - - - -
658B GLU* 4.8 4.9 - - - +
651D GLU 3.1 9.6 + - - -
652D PHE 2.8 17.7 + - - -
654D LYS* 1.3 73.4 - - - +
656D LYS* 1.3 74.5 + - - +
657D ARG 3.1 5.9 + - - -
658D GLU* 4.3 6.2 + - - +
659D GLU* 4.4 8.1 - - - +
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Residues in contact with LYS 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ARG* 5.4 0.7 - - - +
652A PHE* 6.4 0.2 - - - -
656A LYS* 4.8 13.5 - - - +
589D PHE* 4.3 6.3 - - + -
617D TYR* 4.8 3.4 - - + -
640D PRO* 4.6 17.8 - - + +
652D PHE* 3.2 47.8 + - + +
653D LEU* 3.2 6.9 + - - +
655D SER* 1.3 86.1 + - - +
657D ARG* 1.3 66.4 + - - +
658D GLU 3.3 2.0 - - - -
659D GLU* 2.9 32.3 + - - +
660D PHE* 3.0 45.1 + - + +
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Residues in contact with ARG 657 (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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569D ILE* 2.9 46.6 + - + +
570D PRO* 3.5 20.5 + - - +
571D TYR* 3.7 16.4 - - - +
572D VAL* 4.3 5.8 - - + -
589D PHE* 3.9 11.4 - - + -
653D LEU 3.2 10.2 + - - +
654D LYS* 3.2 27.4 + - - +
655D SER 3.1 1.2 - - - -
656D LYS* 1.3 78.4 - - - +
658D GLU* 1.3 79.1 + - - +
660D PHE* 3.5 2.9 + - - +
661D GLN* 3.1 30.2 + - - +
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Residues in contact with GLU 658 (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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658B GLU* 3.7 30.5 - - + +
659B GLU* 3.8 18.8 - - - +
662B GLU* 2.9 47.8 - - + +
666B LYS* 5.0 1.0 + - - -
654D LYS 4.9 0.2 + - - -
655D SER 4.3 4.5 + - - +
656D LYS 3.3 0.4 - - - -
657D ARG* 1.3 90.5 + - - +
659D GLU* 1.3 68.1 + - + +
661D GLN* 3.1 13.8 + - - +
662D GLU* 2.9 22.1 + - + +
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Residues in contact with GLU 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B GLU* 3.9 31.0 - - - +
640D PRO* 3.5 32.2 - - + +
655D SER 4.4 3.0 - - - +
656D LYS* 2.9 48.6 + - - +
658D GLU* 1.3 73.7 - - - +
660D PHE* 1.3 60.3 + - + +
662D GLU* 3.1 9.6 + - - +
663D TYR* 2.9 28.3 + - - +
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Residues in contact with PHE 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569D ILE* 3.7 13.0 - - + -
589D PHE* 3.8 28.3 - + + -
617D TYR* 3.7 29.4 - + - -
620D PHE* 3.4 42.5 - + + -
621D TYR* 3.9 13.2 - + - -
639D LEU* 3.8 8.7 - - + -
640D PRO* 3.8 24.2 - - + -
656D LYS* 3.0 31.6 + - + +
657D ARG* 3.7 5.2 - - - +
659D GLU* 1.3 83.2 - - + +
661D GLN* 1.3 62.4 + - - +
663D TYR* 3.2 8.6 + - - +
664D LEU* 3.2 27.0 + - - +
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Residues in contact with GLN 661 (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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662B GLU* 3.3 30.1 + - - +
666B LYS* 4.9 6.5 - - - +
567D ILE* 4.0 3.1 - - + +
568D SER* 3.4 17.7 - - - -
569D ILE* 3.0 46.8 + - + +
570D PRO* 5.4 0.5 - - - +
657D ARG* 3.1 22.1 + - - +
658D GLU* 3.1 15.1 + - - +
660D PHE* 1.3 75.7 - - - +
662D GLU* 1.3 63.2 + - - +
663D TYR 3.2 0.3 + - - -
664D LEU* 3.2 4.2 + - - +
665D GLN* 3.0 42.2 + - - +
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Residues in contact with GLU 662 (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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661B GLN* 6.1 0.9 - - - +
662B GLU* 3.0 27.2 - - - +
665B GLN* 3.7 27.5 + - - +
658D GLU* 2.9 11.9 + - + +
659D GLU* 3.3 12.1 - - - +
661D GLN* 1.3 75.7 - - - +
663D TYR* 1.3 57.5 + - - +
665D GLN* 3.3 12.4 + - - +
666D LYS* 2.9 67.3 + - - +
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Residues in contact with TYR 663 (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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620D PHE* 4.5 4.7 - + - -
623D LEU* 4.4 8.9 - - + -
624D GLU* 3.2 32.4 - - + +
627D LEU* 4.6 3.8 - - - +
637D ALA* 3.5 35.4 - - - -
638D GLN 3.8 5.4 - - - +
639D LEU* 3.7 48.5 - - + +
640D PRO* 6.2 0.2 - - + -
659D GLU 2.9 12.7 + - - +
660D PHE 3.4 9.2 - - - +
661D GLN 3.1 0.2 - - - -
662D GLU* 1.3 76.2 - - - +
664D LEU* 1.3 80.5 + - + +
666D LYS* 3.1 9.6 + - - +
667D LEU* 2.8 55.5 + - + +
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Residues in contact with LEU 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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567D ILE* 3.5 31.9 - - + -
569D ILE* 4.3 2.7 - - + -
591D ILE* 3.8 29.4 - - + -
620D PHE* 3.9 15.0 - - + -
623D LEU* 4.2 5.2 - - + -
660D PHE 3.2 11.0 + - - +
661D GLN 3.8 0.9 - - - +
663D TYR* 1.3 94.5 - - + +
665D GLN* 1.3 57.7 + - - +
667D LEU* 3.1 15.7 - - + +
668D LEU* 2.9 37.1 + - + +
679D LEU* 4.8 5.8 - - + -
682D PHE* 4.2 18.6 - - + -
683D LEU* 4.4 9.9 - - + -
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Residues in contact with GLN 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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662B GLU* 3.8 15.4 + - - +
666B LYS* 5.3 8.6 - - - +
567D ILE* 3.0 36.9 + - + +
568D SER* 4.7 1.2 - - - +
661D GLN* 3.0 38.0 + - - +
662D GLU* 3.6 18.1 - - - +
664D LEU* 1.3 75.9 - - - +
666D LYS* 1.3 62.7 + - + +
668D LEU* 3.3 16.5 + - + +
669D GLN* 3.3 18.8 + - - +
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Residues in contact with LYS 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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566B LYS* 4.5 13.7 - - - +
665B GLN* 6.1 0.2 - - - +
636D ASP* 2.9 53.1 + - + +
637D ALA* 4.5 4.9 - - + +
638D GLN 5.4 0.2 - - - +
662D GLU* 2.9 55.5 + - - +
663D TYR* 3.9 4.3 - - - +
665D GLN* 1.3 75.0 - - + +
667D LEU* 1.3 63.8 + - - +
669D GLN* 3.3 17.4 + - + +
670D HIS* 3.0 21.7 + - - -
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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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623D LEU* 4.4 1.1 - - + -
627D LEU* 3.8 20.6 - - + -
634D PHE* 5.6 2.7 - - + -
637D ALA* 3.6 25.8 - - + +
663D TYR* 2.8 48.6 + - + +
664D LEU* 3.1 16.6 + - + +
666D LYS* 1.3 73.7 - - - +
668D LEU* 1.3 57.7 + - - +
669D GLN 2.9 9.6 + - - -
670D HIS* 3.2 15.7 + - + +
673D LEU* 3.6 38.7 - - + +
679D LEU* 4.1 21.1 - - + -
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Residues in contact with LEU 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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563D ALA* 3.9 38.2 - - + +
565D TRP* 3.4 30.1 - - + +
567D ILE* 3.6 32.3 - - + +
664D LEU* 2.9 22.1 + - + +
665D GLN* 3.3 8.5 + - + +
667D LEU* 1.3 74.7 - - - +
669D GLN* 1.3 68.8 + - - +
670D HIS 3.4 7.3 - - - +
673D LEU* 5.7 0.4 - - - -
674D SER* 5.6 2.8 - - - -
679D LEU* 3.6 24.5 - - + -
683D LEU* 4.2 15.3 - - + -
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Residues in contact with GLN 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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669B GLN* 4.5 16.6 - - - +
565D TRP 5.7 0.3 - - - +
665D GLN 3.3 17.0 - - - +
666D LYS* 3.4 15.5 - - + +
667D LEU 2.9 1.0 + - - -
668D LEU* 1.3 86.8 - - - +
670D HIS* 1.3 66.2 + - + +
671D PRO* 3.5 7.8 - - - +
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Residues in contact with HIS 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634D PHE* 3.2 51.9 - + + +
635D PRO 4.8 0.2 - - - -
636D ASP* 3.3 29.5 + - - -
637D ALA* 4.1 3.2 - - + +
666D LYS 3.0 28.6 + - - -
667D LEU* 3.2 17.2 + - - +
668D LEU 3.6 8.8 - - - +
669D GLN* 1.3 78.9 - - + +
671D PRO* 1.3 73.3 - - - +
672D GLU* 3.4 12.5 + - - +
673D LEU* 4.0 5.5 - - + +
674D SER* 3.9 8.7 + - - -
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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
------------------------------------------------------------
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