Contacts of the helix formed by residues 687 - 699 (chain D) in PDB entry 1O1F
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 GLU 687 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677D PRO 2.8 11.5 + - - +
678D ASN* 4.1 16.9 - - + +
679D GLU* 3.8 26.6 + - - +
680D THR* 4.7 8.7 + - - +
686D MET* 1.3 72.9 - - - +
688D HIS* 1.3 68.3 + - - +
689D GLU* 4.9 3.2 - - - +
690D LEU* 4.0 21.6 + - + +
691D VAL* 3.0 23.6 + - - +
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Residues in contact with HIS 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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45D GLN* 4.4 18.6 - - + +
46D SER* 3.8 29.6 + - - +
47D PHE 4.1 8.8 + - - -
48D VAL* 5.8 0.4 - - + -
103D LEU* 4.0 23.0 - - + +
104D TYR* 3.6 25.3 - + - -
107D MLY 2.9 48.0 + - + +
686D MET* 3.8 11.9 - - + -
687D GLU* 1.3 69.9 - - - +
689D GLU* 1.3 62.5 - - - +
690D LEU 2.8 10.4 + - - -
691D VAL* 2.8 6.8 + - - +
692D LEU* 2.8 23.4 + - - +
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Residues in contact with GLU 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 3.5 17.3 - - - +
687D GLU* 4.9 3.5 - - - +
688D HIS* 1.3 79.8 - - - +
690D LEU* 1.3 63.4 + - - +
692D LEU* 3.7 11.7 - - + +
693D HIS* 3.1 42.0 + - + +
696D ARG* 5.7 2.9 - - - +
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Residues in contact with LEU 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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180D GLU* 5.5 1.3 - - - +
239D ARG* 4.6 12.1 - - - +
676D ILE* 3.0 22.7 - - + +
677D PRO 3.0 32.8 - - - +
678D ASN* 3.9 8.3 - - - -
679D GLU* 3.8 30.5 - - + +
687D GLU* 3.7 23.3 + - + +
688D HIS 2.8 2.2 + - - -
689D GLU* 1.3 85.0 + - - +
691D VAL* 1.3 50.5 + - - +
693D HIS* 3.4 10.8 - - - +
694D GLN* 2.8 37.7 + - - +
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Residues in contact with VAL 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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103D LEU* 4.5 9.4 - - + -
106D LEU* 4.6 8.7 - - + -
675D ILE* 4.3 16.6 - - + -
676D ILE 4.3 7.6 - - - +
677D PRO* 3.9 13.2 - - + +
686D MET* 3.4 35.7 - - + -
687D GLU 3.0 18.2 - - - +
688D HIS 2.8 7.6 + - - +
690D LEU* 1.3 70.9 - - - +
692D LEU* 1.3 66.9 + - - +
694D GLN* 3.1 8.0 + - - +
695D LEU* 2.9 43.6 + - + +
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Residues in contact with LEU 692 (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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46D SER* 3.6 34.3 - - - +
47D PHE* 4.1 14.4 - - + -
99D GLU* 4.2 28.9 - - + +
103D LEU* 3.6 35.2 - - + -
688D HIS 2.8 9.6 + - - +
689D GLU* 3.7 10.8 - - + +
691D VAL* 1.3 76.5 - - - +
693D HIS* 1.3 65.9 + - - +
695D LEU* 3.1 21.4 + - + +
696D ARG* 3.0 36.3 + - - +
701D LEU* 4.8 0.9 - - + -
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Residues in contact with HIS 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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180D GLU* 5.0 8.3 - - - +
469D ILE* 5.1 11.9 - - + +
689D GLU* 3.1 37.1 + - + +
690D LEU* 3.4 13.4 - - - +
692D LEU* 1.3 76.8 - - - +
694D GLN* 1.3 67.5 + - + +
696D ARG* 2.8 35.8 + - - +
697D CYS* 3.2 27.6 + - - -
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Residues in contact with GLN 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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179D GLY* 6.0 0.2 - - - -
180D GLU* 4.0 26.2 + - + +
183D ALA* 5.2 0.2 - - - +
674D CYS 4.6 3.2 - - - +
675D ILE* 4.1 14.8 - - + -
676D ILE* 2.7 58.6 + - - +
690D LEU* 2.8 33.7 + - - +
691D VAL* 3.4 11.5 - - - +
693D HIS* 1.3 75.6 - - + +
695D LEU* 1.3 54.2 + - - +
697D CYS* 3.2 6.1 + - - +
698D ASN* 2.6 50.1 + - - +
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Residues in contact with LEU 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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99D GLU 5.4 0.2 - - - +
102D VAL* 3.8 27.4 - - + -
103D LEU* 4.7 7.4 - - + +
106D LEU* 4.4 13.9 - - + -
675D ILE* 4.7 6.5 - - + -
691D VAL* 2.9 42.8 + - + +
692D LEU* 3.2 25.8 - - + +
694D GLN* 1.3 80.0 - - + +
696D ARG* 1.3 59.6 + - - +
698D ASN* 3.3 20.0 - - - +
700D VAL* 3.5 15.6 + - + -
701D LEU* 3.0 40.5 + - + -
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Residues in contact with ARG 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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47D PHE* 5.2 1.0 - - - -
99D GLU* 2.3 43.8 + - - +
584D TYR* 3.8 15.4 - - - -
585D ALA* 4.4 13.0 - - - +
689D GLU* 5.5 2.8 + - - +
692D LEU* 3.0 44.9 + - - +
693D HIS* 2.8 26.1 + - + +
695D LEU* 1.3 71.6 - - - +
697D CYS* 1.3 66.3 + - - +
698D ASN 3.1 4.4 + - - -
699D GLY* 3.9 6.8 + - - -
701D LEU* 4.0 16.2 - - + +
702D GLU* 5.4 4.7 + - - +
705D ARG* 6.0 3.3 - - - +
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Residues in contact with CYS 697 (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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178D THR* 5.8 1.4 - - - +
180D GLU* 5.9 2.9 - - - +
466D GLY* 5.7 1.6 - - - -
467D PHE* 3.7 32.5 + - + +
468D GLU* 5.8 0.2 - - - -
469D ILE* 4.1 21.1 - - - -
484D ASN* 6.0 0.3 - - - -
584D TYR* 3.2 17.5 + - - -
585D ALA* 3.9 27.4 - - + -
693D HIS* 3.2 25.1 + - - +
694D GLN* 3.2 5.6 + - - +
696D ARG* 1.3 81.0 - - - +
698D ASN* 1.3 62.1 + - - +
699D GLY 3.4 0.2 - - - -
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Residues in contact with ASN 698 (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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122D PHE* 4.7 0.9 - - - -
178D THR* 4.8 11.4 + - - +
179D GLY* 5.4 3.2 - - - -
488D GLN* 3.9 4.5 - - - +
673D ARG* 3.2 54.8 + - + +
674D CYS 4.8 5.9 + - - -
675D ILE* 3.7 22.2 - - - +
694D GLN* 2.6 33.2 + - - +
695D LEU* 3.3 16.4 + - - +
697D CYS* 1.3 77.7 - - - +
699D GLY* 1.3 57.8 + - - +
700D VAL* 3.4 19.6 - - + +
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Residues in contact with GLY 699 (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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122D PHE* 3.5 14.8 - - - -
488D GLN* 3.5 25.1 - - - -
491D PHE* 4.7 1.6 - - - -
584D TYR* 5.4 1.3 - - - -
695D LEU 3.8 1.8 + - - -
696D ARG 3.9 5.7 + - - -
697D CYS 3.4 2.2 - - - -
698D ASN* 1.3 77.4 - - - +
700D VAL* 1.3 58.5 + - - +
701D LEU 3.3 2.9 - - - -
702D GLU* 2.9 9.7 + - - +
703D GLY* 2.8 26.7 + - - -
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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
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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