Contacts of the helix formed by residues 669 - 684 (chain B) in PDB entry 1OH7
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 THR 669 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ASN* 4.5 11.2 - - - +
617A MET* 6.5 1.3 - - + -
670B PHE* 1.3 61.5 - - - +
671B MET* 3.5 14.3 + - + +
672B VAL* 3.2 35.0 + - + +
673B GLU* 3.6 15.8 + - - +
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Residues in contact with PHE 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ASN* 3.9 23.0 + - + +
728A HIS* 5.8 0.2 - + - -
772A GLY* 3.9 15.5 - - - -
775A VAL* 3.6 36.3 - - + -
669B THR* 1.3 71.4 - - - +
671B MET* 1.3 62.5 + - - +
673B GLU* 3.2 13.5 + - - +
674B MET* 3.0 54.8 + - + +
696B GLY* 4.9 2.5 - - - -
697B ARG 3.7 20.4 - - - +
698B GLY* 3.5 23.5 - - - +
699B THR* 3.4 31.9 - - + -
707B LEU* 4.5 4.0 - - + -
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Residues in contact with MET 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ASN* 4.6 4.6 + - - +
617A MET* 3.5 35.4 - - + +
775A VAL* 3.7 27.8 - - + +
778A LEU* 5.2 9.2 - - + -
779A ALA* 3.9 21.5 - - + -
669B THR* 3.1 14.6 - - + +
670B PHE* 1.3 80.9 - - - +
672B VAL* 1.3 58.9 + - + +
674B MET* 3.2 6.5 + - - +
675B THR* 3.0 50.8 + - - +
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Residues in contact with VAL 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B ARG* 6.2 0.2 - - - +
669B THR* 3.2 23.0 + - + +
671B MET* 1.3 75.9 - - + +
673B GLU* 1.3 62.1 + - - +
675B THR* 3.8 6.5 - - - -
676B GLU* 3.0 49.6 + - + +
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Residues in contact with GLU 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B ARG* 3.4 40.5 + - - +
669B THR 3.6 9.8 + - - +
670B PHE* 3.2 12.6 + - - +
672B VAL* 1.3 79.4 - - - +
674B MET* 1.3 66.4 + - + +
676B GLU* 3.7 1.7 + - - +
677B THR* 2.7 36.3 + - - -
693B ASP 3.7 10.6 - - - +
694B GLU 3.7 6.8 - - - +
695B ILE* 3.8 17.0 - - + -
696B GLY 3.3 19.2 + - - -
697B ARG* 3.4 21.2 + - - +
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Residues in contact with MET 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A VAL* 5.2 0.9 - - + +
776A ALA* 3.9 24.5 - - - -
779A ALA* 3.9 14.8 - - + -
781A VAL* 3.5 13.3 - - + +
670B PHE* 3.0 56.3 + - + +
671B MET* 3.2 10.1 + - - +
673B GLU* 1.3 100.1 - - + +
675B THR* 1.3 55.0 + - - +
677B THR* 3.5 8.0 - - - +
678B ALA* 2.8 33.6 + - - +
695B ILE* 4.3 18.2 - - + -
696B GLY* 4.4 4.0 - - - +
707B LEU* 4.5 13.9 - - + -
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Residues in contact with THR 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A ALA* 3.2 29.2 - - - +
671B MET* 3.0 24.9 + - - +
672B VAL* 3.8 7.8 - - - -
673B GLU 3.3 0.2 - - - -
674B MET* 1.3 75.6 - - - +
676B GLU* 1.3 64.5 + - + +
678B ALA* 3.4 1.9 + - - +
679B ASN* 3.1 22.5 + - - +
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Residues in contact with GLU 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ALA* 3.5 28.7 - - + +
275B ARG* 4.9 5.2 + - - -
276B ASN* 4.8 4.7 + - - -
655B THR 4.9 0.5 - - - +
656B ARG* 3.1 43.2 + - + -
672B VAL* 3.0 34.9 + - + +
675B THR* 1.3 76.9 - - + +
677B THR* 1.3 61.0 + - - +
679B ASN* 3.2 9.4 + - - +
680B ILE* 3.1 28.3 + - + +
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Residues in contact with THR 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A VAL* 5.2 5.2 - - + -
656B ARG* 4.3 3.5 - - - +
673B GLU 2.7 23.5 + - - -
674B MET* 3.5 13.6 - - + +
675B THR 3.3 0.2 - - - -
676B GLU* 1.3 72.8 - - - +
678B ALA* 1.3 64.6 + - - +
680B ILE* 3.2 11.8 + - - +
681B LEU* 3.2 40.6 + - + +
692B MET* 4.0 15.0 - - + +
695B ILE* 3.6 23.6 - - + +
711B CYS* 3.8 18.6 - - - -
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Residues in contact with ALA 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A ALA 3.5 10.1 - - - +
780A GLY 3.4 24.9 - - - +
781A VAL* 3.4 19.5 - - - +
782A PRO* 4.4 3.7 - - - +
674B MET 2.8 18.8 + - - +
675B THR 3.6 5.2 - - - +
676B GLU 3.2 0.2 - - - -
677B THR* 1.3 75.8 - - - +
679B ASN* 1.3 61.3 + - - +
681B LEU* 3.4 2.7 + - - +
682B HIS* 3.1 31.6 + - + -
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Residues in contact with ASN 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLU* 3.6 36.6 + - - +
270B ASP* 4.9 15.1 - - - +
654B PHE* 3.7 14.8 - - - -
675B THR 3.1 12.8 + - - +
676B GLU* 3.5 11.4 - - - +
678B ALA* 1.3 76.0 - - - +
680B ILE* 1.3 65.5 + - + +
682B HIS* 3.4 1.7 + - - -
683B ASN* 2.7 40.8 + - - +
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Residues in contact with ILE 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B PHE* 3.5 33.9 - - + -
655B THR 5.2 0.4 - - - +
656B ARG* 3.7 32.1 - - + +
676B GLU* 3.1 16.8 + - + +
677B THR* 3.2 9.8 + - - +
679B ASN* 1.3 76.6 - - - +
681B LEU* 1.3 58.5 + - + +
684B ALA* 3.0 36.0 + - + +
690B VAL* 3.6 35.7 - - + -
691B LEU 5.1 0.2 - - - +
692B MET* 3.9 19.7 - - - -
715B LEU* 4.2 10.8 - - + -
719B ILE* 4.1 0.2 - - - +
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Residues in contact with LEU 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781A VAL* 4.5 6.5 - - + -
782A PRO* 3.7 36.0 - - + +
785A VAL* 4.6 3.8 - - + -
677B THR* 3.2 36.7 + - + +
678B ALA* 3.4 0.4 + - - -
679B ASN 3.2 0.4 - - - -
680B ILE* 1.3 78.3 - - + +
682B HIS* 1.3 63.5 + - - +
683B ASN 3.7 0.2 + - - -
684B ALA 4.5 1.4 + - - +
692B MET* 6.2 0.2 - - - -
711B CYS* 4.0 16.6 - - - +
714B ASN* 3.5 29.7 + - + +
715B LEU* 3.8 32.8 - - + -
718B LYS* 4.5 11.6 + - - -
719B ILE* 3.6 15.7 - - - +
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Residues in contact with HIS 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780A GLY* 3.0 23.4 + - - -
782A PRO* 3.9 28.5 - - + +
678B ALA* 3.1 22.3 + - + +
679B ASN* 5.1 0.9 - - - -
680B ILE 3.4 0.2 - - - -
681B LEU* 1.3 78.7 - - - +
683B ASN* 1.3 73.3 + - - +
684B ALA 3.8 1.1 - - - +
718B LYS* 5.8 1.1 + - - -
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Residues in contact with ASN 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ASP* 4.3 14.0 - - - +
164B GLU* 5.2 11.8 + - - +
652B ARG* 3.1 42.9 + - - +
654B PHE* 3.8 7.6 - - + -
679B ASN* 2.7 46.3 + - - +
682B HIS* 1.3 95.2 - - - +
684B ALA* 1.3 62.8 + - - +
685B THR* 4.0 4.0 - - - +
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Residues in contact with ALA 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B PHE* 3.7 14.6 - - + -
680B ILE* 3.0 22.1 + - + +
681B LEU 4.5 1.8 + - - +
682B HIS 3.8 1.2 - - - +
683B ASN* 1.3 80.8 + - - +
685B THR* 1.3 63.5 + - - +
688B SER* 3.6 11.0 - - - +
690B VAL* 4.2 12.8 - - + -
718B LYS* 5.3 5.0 + - - -
719B ILE* 3.6 31.3 - - + +
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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
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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