Contacts of the helix formed by residues 650 - 670 (chain D) in PDB entry 7C17
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 LYS 650 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646D ILE* 3.8 23.1 - - + -
647D PRO* 3.3 31.2 + - + +
648D GLU 3.3 4.2 + - - -
649D LYS* 1.3 76.1 - - - +
651D HIS* 1.3 66.9 + - - +
652D GLU 3.3 1.3 - - - -
653D ILE* 3.4 5.6 + - - +
654D ILE* 3.3 38.5 + - + +
693D VAL* 4.1 11.4 - - + +
741D ALA 3.9 13.7 - - - -
742D GLY* 4.3 9.9 - - - -
743D MET* 4.4 6.1 - - - +
760D THR 3.4 24.5 + - - -
761D ALA* 4.3 1.6 - - - +
762D ASN* 3.6 29.6 + - - +
765D GLU* 6.0 0.2 - - - +
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Residues in contact with HIS 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D GLU 3.7 20.8 + - - -
649D LYS* 5.2 0.7 - - - -
650D LYS* 1.3 77.5 - - - +
652D GLU* 1.3 80.7 + - + +
654D ILE* 3.4 10.7 + - - +
655D SER* 2.8 34.7 + - - +
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Residues in contact with GLU 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649D LYS* 3.3 42.5 - - + +
651D HIS* 1.3 91.2 + - + +
653D ILE* 1.3 67.3 + - + +
655D SER* 3.7 7.0 - - - -
656D GLU* 2.9 42.6 + - + +
692D ARG* 5.2 5.6 + - - +
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Residues in contact with ILE 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649D LYS* 3.3 25.1 - - + +
650D LYS 3.4 8.2 + - - +
651D HIS 3.3 0.2 - - - -
652D GLU* 1.3 82.5 - - + +
654D ILE* 1.3 57.2 + - - +
656D GLU* 3.4 5.9 + - - +
657D ALA* 2.9 28.1 + - - +
689D ALA* 3.9 31.3 - - + +
692D ARG* 3.9 35.0 - - + +
693D VAL* 3.8 35.7 - - + +
696D ALA* 4.2 8.1 - - + -
743D MET* 4.5 6.1 - - + -
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Residues in contact with ILE 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D LYS* 3.3 32.9 + - + +
651D HIS* 3.9 9.2 - - - +
652D GLU 3.4 0.2 - - - -
653D ILE* 1.3 75.8 - - - +
655D SER* 1.3 56.5 + - - +
657D ALA* 3.4 6.1 + - - +
658D GLU* 2.9 29.3 + - + +
686D TRP* 5.2 3.5 - - + -
743D MET* 3.9 19.5 - - + -
760D THR* 3.4 48.9 - - + +
761D ALA* 5.2 0.9 - - - -
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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
----------------------------------------------------------
651D HIS* 2.8 26.1 + - - +
652D GLU* 3.7 8.6 - - - -
654D ILE* 1.3 77.5 - - - +
656D GLU* 1.3 57.7 + - - +
658D GLU* 3.3 10.2 + - - +
659D ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D GLU* 2.9 27.8 + - + +
653D ILE* 3.8 3.4 - - - +
655D SER* 1.3 75.7 - - - +
657D ALA* 1.3 59.5 + - - +
659D ALA* 3.4 7.6 + - - +
660D GLU* 2.9 34.5 + - + +
692D ARG* 2.8 43.3 + - - +
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Residues in contact with ALA 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653D ILE 2.9 18.3 + - - +
654D ILE* 3.7 6.7 - - - +
656D GLU* 1.3 73.0 - - - +
658D GLU* 1.3 61.2 + - - +
660D GLU* 3.3 6.3 + - - +
661D VAL* 2.9 35.8 + - + +
685D ILE* 5.6 2.0 - - + +
686D TRP* 4.0 28.3 - - + -
689D ALA* 4.2 20.0 - - + -
743D MET* 6.1 0.2 - - + -
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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
----------------------------------------------------------
633C LEU* 3.9 22.5 - - - +
644C LEU* 4.6 11.4 - - + +
654D ILE* 2.9 18.5 + - + +
655D SER* 3.3 9.5 + - - +
657D ALA* 1.3 74.3 - - - +
659D ALA* 1.3 65.7 + - - +
661D VAL* 3.3 14.0 - - + +
662D ALA* 2.9 35.4 + - - +
686D TRP* 5.5 1.3 - - - -
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Residues in contact with ALA 659 (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 SER 2.9 16.3 + - - +
656D GLU* 3.7 9.2 - - - +
658D GLU* 1.3 83.2 + - - +
660D GLU* 1.3 56.0 + - + +
662D ALA* 3.4 7.3 + - - +
663D GLU* 2.9 28.5 + - - +
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Residues in contact with GLU 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D GLU* 2.9 21.5 + - + +
657D ALA* 3.6 8.5 - - - +
658D GLU 3.3 0.2 - - - -
659D ALA* 1.3 77.7 - - + +
661D VAL* 1.3 57.4 + - - +
663D GLU* 3.2 20.9 + - - +
664D ILE* 2.9 35.2 + - - +
685D ILE* 3.8 34.5 - - + +
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Residues in contact with VAL 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644C LEU* 6.2 3.4 - - + -
657D ALA* 2.9 20.5 + - + +
658D GLU* 3.3 24.0 - - + +
660D GLU* 1.3 72.4 - - - +
662D ALA* 1.3 60.8 + - - +
664D ILE* 3.7 8.3 - - + +
665D GLN* 2.9 29.3 + - - +
682D VAL* 3.7 18.6 - - + -
685D ILE* 3.8 9.4 - - + -
686D TRP* 3.4 33.7 - - + +
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Residues in contact with ALA 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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658D GLU* 2.9 25.4 + - - +
659D ALA* 3.6 8.1 - - - +
661D VAL* 1.3 75.2 - - - +
663D GLU* 1.3 58.6 + - - +
665D GLN* 3.3 6.7 + - - +
666D GLU* 2.9 35.9 + - + +
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Residues in contact with GLU 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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659D ALA 2.9 13.5 + - - +
660D GLU* 3.5 26.3 - - - +
662D ALA* 1.3 78.8 - - - +
664D ILE* 1.3 58.0 + - + +
666D GLU* 3.4 6.0 + - - +
667D GLN* 2.9 53.4 + - + +
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Residues in contact with ILE 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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660D GLU* 2.9 23.3 + - - +
661D VAL* 3.7 8.1 - - - +
663D GLU* 1.3 80.0 - - + +
665D GLN* 1.3 56.7 + - - +
667D GLN* 3.3 21.8 + - + +
668D PHE* 2.9 27.5 + - - +
673D VAL* 5.8 0.5 - - - +
678D ARG* 3.7 36.7 - - + +
681D LYS* 3.9 27.1 - - + -
682D VAL* 4.5 9.9 - - + -
685D ILE* 3.8 21.3 - - + -
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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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643C SER* 6.3 1.0 - - - -
661D VAL 2.9 17.6 + - - +
662D ALA* 3.7 8.1 - - - +
663D GLU 3.3 0.2 - - - -
664D ILE* 1.3 77.5 - - - +
666D GLU* 1.3 64.9 + - - +
668D PHE* 3.2 32.4 + - - -
669D GLN* 2.9 46.8 + - - +
678D ARG* 5.0 13.1 - - - +
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Residues in contact with GLU 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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662D ALA* 2.9 22.8 + - + +
663D GLU* 3.8 6.7 - - - +
665D GLN* 1.3 83.1 - - - +
667D GLN* 1.3 53.6 + - + +
669D GLN* 3.2 28.8 + - - +
670D SER* 2.4 39.3 + - - +
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Residues in contact with GLN 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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663D GLU* 2.9 45.7 + - + +
664D ILE* 3.6 22.4 - - + +
666D GLU* 1.3 75.9 - - + +
668D PHE* 1.3 58.5 + - - +
670D SER* 2.9 19.1 - - - +
672D LEU* 3.8 29.0 + - + +
673D VAL* 3.9 20.5 + - + +
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Residues in contact with PHE 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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664D ILE 2.9 16.0 + - - +
665D GLN* 3.2 26.2 + - - +
667D GLN* 1.3 78.0 - - - +
669D GLN* 1.3 70.3 + - + +
670D SER 4.3 1.9 - - - +
671D GLY* 4.5 4.3 - - - -
673D VAL* 4.5 11.3 - - - +
674D THR 4.1 13.7 - - - -
675D ALA* 3.9 30.3 - - + -
678D ARG* 3.5 33.2 - - + -
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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
----------------------------------------------------------
665D GLN* 2.9 37.3 + - - +
666D GLU* 3.2 32.3 + - - +
668D PHE* 1.3 80.6 - - + +
670D SER* 1.3 63.8 + - - +
671D GLY* 3.2 4.5 + - - -
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Residues in contact with SER 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666D GLU* 2.4 28.3 + - - +
667D GLN* 2.9 24.5 - - - +
669D GLN* 1.3 73.4 - - - +
671D GLY* 1.3 64.3 + - - +
672D LEU* 3.1 2.9 + - - +
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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