Contacts of the helix formed by residues 653 - 664 (chain D) in PDB entry 4OIR
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 PHE 653 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644D LEU* 4.5 14.1 - - + -
649D ALA* 2.9 28.3 + - - +
650D LEU 3.8 1.3 - - - -
652D LEU* 1.3 78.3 - - + +
654D LYS* 1.3 64.8 + - - +
655D PRO* 3.3 5.6 - - - -
656D PHE* 2.9 33.0 + + - +
657D LEU* 3.1 7.9 + - - -
691D LEU* 4.2 12.8 - - + -
694D VAL* 4.2 11.2 - - + -
695D ILE* 3.7 31.2 - - + -
698D LYS* 4.0 27.1 - - + -
699D VAL 5.1 1.8 - - - -
700D VAL* 3.8 28.9 - - + -
718D PRO* 4.9 5.4 - - + -
749D VAL* 3.6 29.8 - - + -
756D GLN* 6.0 0.4 - - - -
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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
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1009C SER* 4.2 3.8 - - - +
650D LEU* 3.1 23.6 + - - +
651D GLU* 3.5 35.9 + - - +
652D LEU 3.3 1.4 - - - -
653D PHE* 1.3 74.7 - - - +
655D PRO* 1.3 70.5 - - + +
657D LEU* 3.1 7.0 + - - +
658D LEU* 2.9 32.1 + - + +
674D ARG* 3.6 52.2 + - - +
677D LEU* 3.8 39.1 + - + +
678D GLU* 5.0 3.3 - - - +
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Residues in contact with PRO 655 (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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1009C SER* 4.4 4.5 - - - -
1067C TYR* 3.7 24.0 - - + -
1070C ILE* 3.6 24.5 - - + -
1071C ILE* 3.6 24.6 - - + +
625D TYR* 3.8 29.6 - - + +
652D LEU 4.4 0.2 - - - +
653D PHE 3.4 5.4 - - - +
654D LYS* 1.3 92.6 - - + +
656D PHE* 1.3 59.1 + - + +
658D LEU* 3.1 9.2 + - + +
659D LYS* 2.9 28.4 + - - +
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Residues in contact with PHE 656 (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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1070C ILE* 3.7 42.0 - - + -
625D TYR* 5.5 1.3 - + - -
652D LEU 5.2 1.8 - - - -
653D PHE* 2.9 33.9 + + - +
655D PRO* 1.3 82.1 - - + +
657D LEU* 1.3 56.9 + - - +
659D LYS* 3.3 7.9 + - - +
660D LYS* 2.9 25.6 + - - +
694D VAL* 3.5 28.9 - - + +
698D LYS* 3.5 35.4 - - - -
749D VAL* 5.1 2.7 - - + -
751D LEU* 4.3 25.1 - - + -
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Residues in contact with LEU 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D LEU* 3.9 26.7 - - + +
653D PHE 3.1 7.4 + - - +
654D LYS* 3.1 11.1 + - - +
656D PHE* 1.3 77.1 - - - +
658D LEU* 1.3 60.1 + - - +
660D LYS* 3.5 0.6 + - + -
661D MET* 2.9 47.3 + - + +
677D LEU* 3.6 25.8 - - + -
687D VAL* 3.6 13.5 - - + +
690D ALA* 4.0 11.0 - - + -
691D LEU* 3.6 48.2 - - + +
694D VAL* 3.9 6.0 - - + +
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Residues in contact with LEU 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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1067C TYR* 3.8 10.1 - - - +
1071C ILE* 4.4 2.7 - - + -
654D LYS* 2.9 22.6 + - + +
655D PRO* 3.4 11.0 - - + +
657D LEU* 1.3 76.4 - - - +
659D LYS* 1.3 57.2 + - - +
661D MET* 3.1 24.5 + - + +
662D GLU* 2.9 28.6 + - - +
670D VAL* 3.9 29.8 - - + -
673D ALA* 3.7 7.6 - - + +
674D ARG* 3.4 64.4 - - + +
677D LEU* 4.4 7.9 - - + -
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Residues in contact with LYS 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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1070C ILE 3.9 12.8 - - - +
1071C ILE 3.5 26.2 + - - +
1072C LYS 3.7 20.5 + - - +
1073C GLY* 4.0 10.8 - - - -
655D PRO 2.9 12.6 + - - +
656D PHE* 3.5 10.5 - - - +
658D LEU* 1.3 77.5 - - - +
660D LYS* 1.3 59.2 + - + +
662D GLU* 3.2 19.0 + - + +
663D GLU* 2.9 66.2 + - - +
670D VAL* 5.5 1.1 - - - -
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Residues in contact with LYS 660 (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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656D PHE 2.9 7.1 + - - +
657D LEU 4.1 2.0 - - - +
659D LYS* 1.3 77.4 - - - +
661D MET* 1.3 60.0 + - - +
662D GLU 3.4 0.2 - - - -
663D GLU* 3.6 35.5 + - + +
664D LYS* 3.3 27.6 + - - +
666D ILE* 4.9 0.5 - - - +
690D ALA* 4.1 22.2 - - + +
693D GLU* 4.2 21.1 + - - +
694D VAL* 3.6 38.1 - - + +
58E PRO* 4.4 21.2 - - - +
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Residues in contact with MET 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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657D LEU* 2.9 45.1 + - + +
658D LEU* 3.1 24.7 + - + +
660D LYS* 1.3 78.9 - - - +
662D GLU* 1.3 57.1 + - - +
664D LYS 3.0 18.7 - - - +
666D ILE* 3.6 30.2 + - + -
667D ALA* 3.3 18.5 + - + -
673D ALA* 3.8 18.6 - - + +
676D MET* 4.8 7.0 - - - +
677D LEU* 3.6 34.5 - - + -
687D VAL* 4.5 21.5 - - + -
690D ALA* 4.7 2.0 - - + -
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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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1071C ILE 5.9 0.7 - - - -
658D LEU 2.9 12.0 + - - +
659D LYS* 3.2 22.9 + - + +
661D MET* 1.3 74.2 - - - +
663D GLU* 1.3 64.8 + - - +
664D LYS 3.0 7.4 - - - +
667D ALA* 3.8 9.6 - - - +
668D PRO 3.8 17.5 - - - +
669D ASN* 3.3 15.1 - - - +
670D VAL* 3.1 35.7 + - + +
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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 LYS* 2.9 52.9 + - - +
660D LYS* 3.6 41.7 + - + +
661D MET 3.3 0.2 - - - -
662D GLU* 1.3 77.8 - - - +
664D LYS* 1.3 60.1 + - + +
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Residues in contact with LYS 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 LYS* 3.3 19.9 + - + +
661D MET 3.0 7.9 - - - +
662D GLU 3.0 15.7 - - - +
663D GLU* 1.3 80.7 - - + +
665D GLY* 1.3 60.2 + - - +
666D ILE* 3.2 30.7 + - + -
667D ALA 3.9 3.8 - - - +
686D GLU 5.2 1.2 + - - -
689D ASP* 4.7 4.0 - - - +
690D ALA* 4.2 15.0 - - + +
693D GLU* 2.5 45.1 + - - -
51E LEU* 6.4 0.2 - - - +
52E GLU* 5.7 3.5 + - - -
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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