Contacts of the strand formed by residues 830 - 843 (chain I) in PDB entry 6ALH
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 830 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690I VAL* 3.9 13.2 - - + +
691I PRO* 3.1 24.7 + - - +
692I THR* 4.7 1.9 - - - +
693I LEU 4.8 2.5 - - - +
763I THR* 5.8 0.2 - - - -
764I CYS* 5.9 0.2 - - - +
828I PHE 4.1 3.6 - - - -
829I THR* 1.3 75.0 - - - +
831I ILE* 1.3 77.0 + - - +
832I HIS* 3.9 20.0 - - + +
1057I LYS* 3.5 6.2 - - - +
1058I ARG* 2.9 40.6 + - + +
1234I LYS* 3.4 28.5 - - + +
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Residues in contact with ILE 831 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G TYR* 4.2 23.8 - - + +
79G LEU* 4.4 9.6 - - + -
692I THR 6.1 0.7 - - - +
693I LEU* 5.0 16.6 - - + -
756I TYR* 4.0 29.2 - - + +
763I THR* 3.7 1.0 - - - -
764I CYS* 3.4 44.4 + - + +
830I THR* 1.3 87.2 + - - +
832I HIS* 1.3 81.5 + - - +
833I ILE* 4.5 8.7 - - + -
1055I ALA* 4.7 10.1 - - + -
1056I VAL 3.4 7.4 - - - +
1057I LYS* 5.2 3.6 - - + -
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Residues in contact with HIS 832 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690I VAL* 4.7 6.7 - - - +
761I GLN 6.0 0.2 - - - -
762I ASN* 3.3 17.3 - - + +
763I THR* 4.5 8.1 - - + +
830I THR* 3.9 20.3 - - + +
831I ILE* 1.3 88.6 - - - +
833I ILE* 1.3 64.5 + - - +
834I GLN* 4.2 3.8 - - + -
1054I LEU 4.1 0.2 - - - -
1055I ALA* 3.1 6.2 - - - -
1056I VAL* 2.9 34.2 + - + +
1058I ARG* 3.0 51.0 + - + +
1236I ASN* 6.2 0.6 - - + +
1238I LEU* 3.6 25.5 - - + +
1241I ASP* 4.4 11.2 + - - -
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Residues in contact with ILE 833 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756I TYR* 4.9 3.6 - - + -
757I THR* 3.3 36.6 - - - +
758I ARG* 3.9 15.6 - - + +
762I ASN* 3.1 34.9 + - - +
763I THR 4.1 12.5 + - - +
764I CYS* 4.5 9.0 - - + -
831I ILE* 4.5 11.0 - - + -
832I HIS* 1.3 78.8 - - - +
834I GLN* 1.3 63.9 + - - +
835I GLU 4.1 0.2 + - - -
929I ILE* 4.6 12.1 - - + -
1053I TYR* 3.9 31.2 - - + -
1054I LEU 2.9 10.5 - - - +
1055I ALA* 4.5 7.4 - - + -
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Residues in contact with GLN 834 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762I ASN* 4.5 13.2 - - + +
832I HIS* 4.2 3.6 - - + -
833I ILE* 1.3 80.6 - - - +
835I GLU* 1.3 59.9 + - - +
836I LEU* 3.7 23.6 + - + +
921I PRO* 4.3 9.9 - - - +
924I VAL* 4.3 23.7 - - - +
1052I VAL 3.5 1.7 - - - +
1053I TYR* 3.5 5.2 - - - -
1054I LEU* 2.9 38.2 + - + +
1056I VAL* 4.9 10.4 - - + +
1058I ARG* 4.1 25.5 - - - +
1241I ASP* 5.4 3.0 + - - -
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Residues in contact with GLU 835 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758I ARG* 3.2 44.5 + - - +
762I ASN* 4.8 0.8 + - - -
833I ILE 4.1 0.8 + - - -
834I GLN* 1.3 70.4 - - - +
836I LEU* 1.3 63.2 + - - +
837I ALA* 3.6 5.3 + - + +
1051I LYS* 3.2 43.6 + - + +
1052I VAL 3.8 3.6 - - - +
1053I TYR* 3.4 31.3 + - + -
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Residues in contact with LEU 836 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834I GLN* 3.9 30.5 - - + +
835I GLU* 1.3 73.4 - - - +
837I ALA* 1.3 60.6 + - - +
883I LEU* 3.7 27.6 - - + -
918I LEU* 4.3 16.8 - - + +
919I ARG 3.8 12.8 - - - +
920I VAL* 4.4 2.2 - - - -
921I PRO* 3.6 31.0 - - + -
1050I VAL 3.7 0.9 - - - +
1051I LYS* 3.4 4.9 - - - -
1052I VAL* 2.9 38.7 + - + +
1054I LEU* 3.8 20.2 - - + -
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Residues in contact with ALA 837 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835I GLU* 3.6 5.4 + - + +
836I LEU* 1.3 75.2 - - - +
838I CYS* 1.3 65.9 + - - +
839I VAL* 5.5 4.9 - - + -
918I LEU* 3.4 18.4 - - - +
1049I ILE* 5.4 5.2 - - + -
1050I VAL 3.6 4.0 - - - +
1051I LYS* 4.7 13.2 - - + +
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Residues in contact with CYS 838 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837I ALA* 1.3 77.1 - - - +
839I VAL* 1.3 68.1 + - - +
850I ILE* 5.8 2.5 - - - -
884I VAL* 4.3 18.8 - - + -
886I LYS* 3.9 35.7 - - - -
918I LEU* 3.7 29.4 - - + -
1048I LYS 4.2 0.2 - - - +
1049I ILE* 3.4 5.0 - - - +
1050I VAL* 2.9 41.0 + - + +
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Residues in contact with VAL 839 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837I ALA* 5.5 5.6 - - + -
838I CYS* 1.3 82.0 - - - +
840I SER* 1.3 62.2 + - - +
841I ARG* 3.4 43.5 - - + +
848I GLU* 3.6 2.1 - - - +
850I ILE* 5.2 1.1 - - - +
886I LYS* 3.4 27.3 - - + +
1046I VAL* 4.1 9.4 - - + -
1048I LYS 3.6 3.8 - - - -
1049I ILE* 3.7 25.6 - - + -
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Residues in contact with SER 840 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839I VAL* 1.3 75.2 - - - +
841I ARG* 1.3 58.1 + - - +
848I GLU* 2.8 27.4 + - - +
850I ILE* 3.8 14.0 - - - +
1046I VAL* 3.6 2.6 - - - +
1047I LEU* 2.4 46.4 + - - +
1048I LYS* 2.9 38.1 + - - +
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Residues in contact with ARG 841 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839I VAL* 3.4 36.5 - - + +
840I SER* 1.3 79.4 + - - +
842I ASP* 1.3 66.3 + - - +
843I THR* 4.9 8.3 - - + -
847I PRO* 4.2 0.3 - - - +
848I GLU* 2.5 47.9 + - - +
1044I PRO 5.7 0.4 - - - +
1045I GLY* 3.3 15.0 - - - +
1046I VAL* 3.7 14.0 - - + +
1047I LEU* 4.3 3.4 - - - +
256J ASP* 3.6 40.2 + - - +
257J GLY* 4.3 18.0 - - - +
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Residues in contact with ASP 842 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841I ARG* 1.3 76.2 - - - +
843I THR* 1.3 83.7 + - - +
846I GLY 3.0 15.8 - - - +
847I PRO* 3.8 19.7 - - + +
848I GLU* 5.0 0.2 - - - -
1045I GLY* 2.8 20.3 + - - +
1047I LEU* 4.8 12.3 - - + +
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Residues in contact with THR 843 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841I ARG* 4.3 9.4 - - + -
842I ASP* 1.3 87.3 + - - +
844I LYS* 1.3 70.7 + - - +
846I GLY 2.9 21.1 + - - +
848I GLU* 4.5 16.5 + - - +
49J PHE* 4.4 22.7 - - + -
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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