Contacts of the helix formed by residues 684 - 696 (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 LYS 684 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B GLN* 6.1 0.2 - - - -
666D ILE* 5.0 1.3 - - + -
676D MET* 3.6 20.8 - - + +
682D ASP 3.8 16.8 - - - -
683D ILE* 1.3 75.6 - - - +
685D ASP* 1.3 66.4 + - - +
686D GLU* 3.3 25.4 - - - +
687D VAL* 3.2 39.6 + - + +
688D TRP* 3.2 9.0 - - - -
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Residues in contact with ASP 685 (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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5B LYS* 5.7 2.9 + - - -
187B GLY* 3.8 19.2 - - - -
188B GLN* 3.8 27.2 + - + +
684D LYS* 1.3 76.1 - - - +
686D GLU* 1.3 72.3 + - + +
688D TRP* 3.2 23.5 + - - +
689D ASP* 3.5 16.7 - - - +
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Residues in contact with GLU 686 (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 LYS* 5.2 1.4 + - - -
666D ILE* 4.0 26.3 - - + +
684D LYS* 3.3 33.4 + - - +
685D ASP* 1.3 86.1 + - + +
687D VAL* 1.3 57.7 + - - +
688D TRP 3.2 0.3 + - - -
689D ASP* 3.3 12.0 + - - +
690D ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D LEU* 4.9 5.8 - - + -
657D LEU* 3.6 7.3 - - + +
661D MET* 4.5 14.8 - - - -
666D ILE* 4.5 9.9 - - + -
676D MET* 3.9 16.6 - - + -
677D LEU* 4.7 12.6 - - + -
683D ILE* 4.0 15.9 - - + -
684D LYS* 3.2 39.9 - - + +
685D ASP 3.2 0.8 - - - -
686D GLU* 1.3 74.7 - - - +
688D TRP* 1.3 74.0 + - + +
690D ALA* 3.4 9.6 - - - +
691D LEU* 2.9 27.0 + - - +
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Residues in contact with TRP 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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185B ARG* 4.5 7.0 - - - +
187B GLY 5.5 0.9 - - - +
188B GLN* 2.9 31.8 + - - +
646D LYS* 3.5 57.2 - - + -
647D ARG* 4.8 8.7 - - + -
650D LEU* 3.8 26.9 - - + -
683D ILE* 3.5 32.6 - - + +
684D LYS 3.2 28.2 + - - -
685D ASP* 3.2 13.6 + - - +
686D GLU 3.1 0.6 - - - -
687D VAL* 1.3 80.0 - - + +
689D ASP* 1.3 62.1 + - - +
691D LEU* 3.2 17.3 + - + +
692D GLU* 2.9 33.7 + - + +
720D LEU* 4.4 5.0 - - + +
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Residues in contact with ASP 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 2.4 47.0 + - - +
187B GLY* 4.5 3.6 - - - -
664D LYS* 5.1 5.2 - - - +
685D ASP* 3.5 23.4 - - - +
686D GLU* 3.3 11.3 + - - +
688D TRP* 1.3 76.0 - - - +
690D ALA* 1.3 58.5 + - - +
692D GLU* 3.2 4.3 + - - +
693D GLU* 2.9 36.0 + - - +
50E THR* 5.9 1.3 - - + -
51E LEU* 3.3 38.2 - - + +
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Residues in contact with ALA 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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657D LEU* 4.0 11.9 - - + -
660D LYS* 4.1 11.5 - - + +
661D MET* 4.7 3.4 - - + -
664D LYS* 4.2 15.8 - - + +
666D ILE* 4.1 17.0 - - + -
686D GLU 2.9 14.5 + - - +
687D VAL* 3.4 14.6 - - - +
689D ASP* 1.3 76.3 - - - +
691D LEU* 1.3 56.9 + - - +
693D GLU* 3.1 6.7 + - - +
694D VAL* 2.9 29.8 + - - +
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Residues in contact with LEU 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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646D LYS 4.2 8.3 - - - +
649D ALA* 4.1 18.6 - - + +
650D LEU* 3.9 29.2 - - + +
653D PHE* 4.2 10.5 - - + -
657D LEU* 3.6 20.8 - - + +
687D VAL 2.9 15.5 + - - +
688D TRP* 3.2 21.1 + - + +
690D ALA* 1.3 71.8 - - - +
692D GLU* 1.3 60.5 + - - +
694D VAL* 3.0 9.0 + - + +
695D ILE* 2.9 49.7 + - + +
720D LEU* 3.9 22.2 - - + -
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Residues in contact with GLU 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 2.6 45.8 + - - +
688D TRP* 2.9 17.2 + - + +
689D ASP 3.3 9.6 - - - +
691D LEU* 1.3 78.0 - - - +
693D GLU* 1.3 61.4 + - + +
695D ILE* 3.7 11.7 + - - +
696D HIS* 3.4 22.0 + - - +
720D LEU* 3.7 29.0 + - + +
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Residues in contact with GLU 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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660D LYS* 4.2 19.3 + - + +
664D LYS* 2.5 43.8 + - - -
689D ASP* 2.9 16.5 + - - +
690D ALA* 3.4 7.4 - - - +
692D GLU* 1.3 74.3 - - + +
694D VAL* 1.3 68.4 + - - +
696D HIS* 3.4 14.9 + - - +
48E MET* 4.0 35.6 - - + +
50E THR* 3.2 29.3 - - + +
52E GLU* 5.3 0.5 - - - +
58E PRO* 4.4 10.8 - - + +
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Residues in contact with VAL 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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653D PHE* 4.2 14.6 - - + -
656D PHE* 3.5 52.3 - - + +
657D LEU* 3.9 7.6 - - - +
660D LYS* 3.6 23.6 - - + +
690D ALA 2.9 17.8 + - - +
691D LEU* 3.2 13.5 - - + +
693D GLU* 1.3 79.1 - - - +
695D ILE* 1.3 70.8 + - + +
696D HIS 3.3 3.1 + - - +
698D LYS* 3.6 16.5 - - - +
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Residues in contact with ILE 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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649D ALA* 5.3 2.2 - - + -
653D PHE* 3.7 37.2 - - + -
691D LEU* 2.9 30.6 + - + +
692D GLU* 3.8 13.2 - - + +
694D VAL* 1.3 73.1 - - + +
696D HIS* 1.3 69.3 + - - +
697D GLY 3.2 0.9 + - - -
698D LYS* 3.0 31.2 + - - +
717D GLN* 5.7 0.2 - - - +
718D PRO* 3.8 37.0 - - + +
719D VAL* 5.2 0.2 - - - -
720D LEU* 4.1 30.3 - - + +
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Residues in contact with HIS 696 (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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692D GLU 3.4 11.6 + - - +
693D GLU 3.5 15.6 - - - +
694D VAL 3.2 5.8 - - - +
695D ILE* 1.3 81.2 - - - +
697D GLY* 1.3 65.0 + - - +
698D LYS* 3.1 5.4 + - - +
47E LYS 4.7 2.8 + - - -
48E MET* 3.9 36.7 - - + +
49E GLN 5.3 0.8 + - - -
57E ASP* 3.0 43.4 + - - -
58E PRO* 4.2 4.1 - - + +
59E ASN* 3.7 14.6 + - - +
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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