Contacts of the helix formed by residues 914 - 925 (chain J) in PDB entry 6PSU
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 ALA 914 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1279I GLU 3.4 26.2 + - - +
1280I ALA* 4.8 1.1 - - - -
1281I TYR 5.3 0.6 + - - -
805J GLN 5.7 0.9 - - - +
807J LEU 4.3 0.7 - - - +
808J VAL* 3.8 12.8 - - + -
912J GLY 3.3 2.8 + - - -
913J GLU* 1.3 72.8 + - - +
915J ILE* 1.3 58.8 + - - +
916J GLY 3.0 3.4 - - - -
917J VAL* 2.8 25.6 + - + +
918J ILE* 3.3 11.8 + - - +
1347J LEU* 4.0 13.2 - - + -
1359J ALA* 3.9 19.7 - - + -
1360J GLY* 5.9 0.2 - - - -
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Residues in contact with ILE 915 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807J LEU* 3.5 17.9 + - + +
809J VAL* 3.5 19.7 - - + +
885J VAL* 4.9 0.7 - - + -
894J VAL* 3.4 30.7 - - + -
899J TYR* 3.8 46.1 + - + -
909J ILE* 4.5 0.4 - - + -
913J GLU* 2.7 28.0 + - + +
914J ALA* 1.3 70.9 - - - +
916J GLY* 1.3 60.7 + - - +
918J ILE* 3.3 11.5 - - + +
919J ALA* 2.9 31.0 + - - +
1255J VAL* 4.2 11.5 - - + +
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Residues in contact with GLY 916 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804J ALA* 3.2 32.2 - - - +
807J LEU* 3.3 18.2 + - - -
914J ALA 2.9 2.0 + - - -
915J ILE* 1.3 83.3 - - - +
917J VAL* 1.3 55.9 + - - +
919J ALA* 3.4 3.1 - - - +
920J ALA* 3.0 27.8 + - - +
1255J VAL* 4.1 7.0 - - - -
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Residues in contact with VAL 917 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276I TRP* 3.5 28.3 - - + +
1279I GLU* 4.5 11.2 - - + +
1280I ALA* 3.8 15.0 - - + +
801J VAL* 4.2 14.8 - - + -
804J ALA 4.2 0.4 + - - -
805J GLN* 3.9 35.1 + - + +
807J LEU 5.0 0.2 + - - -
914J ALA* 2.8 20.2 + - + +
916J GLY* 1.3 70.1 - - - -
918J ILE* 1.3 60.8 + - - +
920J ALA* 3.1 6.6 + - - +
921J GLN* 2.9 37.5 + - + +
1347J LEU* 4.9 3.6 - - + -
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Residues in contact with ILE 918 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1280I ALA* 3.3 32.1 - - + +
431J ARG* 3.7 24.9 - - - +
493J PRO* 4.9 13.7 - - + +
899J TYR* 4.3 13.5 - - - +
902J ASP 5.8 1.1 - - - +
903J LEU* 4.6 7.6 - - + -
913J GLU* 3.9 24.2 - - + +
914J ALA 3.3 2.0 + - - +
915J ILE* 3.3 35.0 - - + +
917J VAL* 1.3 73.7 - - - +
919J ALA* 1.3 59.8 + - - +
921J GLN* 4.1 5.3 - - - +
922J SER* 2.9 32.1 + - - -
1252J HIS* 4.9 5.6 - - + +
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Residues in contact with ALA 919 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915J ILE 2.9 21.0 + - - +
916J GLY 3.4 4.9 - - - +
918J ILE* 1.3 77.8 - - - +
920J ALA* 1.3 60.0 + - - +
922J SER* 2.7 21.0 + - - -
923J ILE* 2.9 18.7 + - - +
1252J HIS* 3.8 30.7 + - + +
1255J VAL* 3.9 17.9 - - + -
1256J ILE* 4.8 5.4 - - + -
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Residues in contact with ALA 920 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797J THR* 4.2 4.9 - - - +
800J LEU* 3.9 17.7 - - + +
801J VAL* 3.3 46.0 - - + +
916J GLY 3.0 13.3 + - - +
917J VAL* 3.1 5.6 + - - +
919J ALA* 1.3 77.1 - - - +
921J GLN* 1.3 58.1 + - - +
923J ILE* 3.8 1.5 - - - +
924J GLY* 2.8 26.9 + - - -
1256J ILE* 4.7 5.5 - - + +
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Residues in contact with GLN 921 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1273I MET 4.5 1.8 + - - -
1276I TRP* 3.2 45.7 + - - +
1277I ALA* 3.5 5.3 - - - +
1280I ALA* 3.6 16.1 - - - +
429J LEU 3.5 23.7 + - - +
430J HIS* 3.9 8.5 - - + +
431J ARG* 3.3 18.7 + - - +
493J PRO* 6.1 1.6 - - + -
797J THR* 4.3 14.8 - - + -
801J VAL* 4.8 4.0 - - + -
917J VAL* 2.9 23.8 + - + +
918J ILE* 4.1 5.3 - - - +
919J ALA 3.3 0.2 - - - -
920J ALA* 1.3 75.9 - - - +
922J SER* 1.3 58.1 + - - +
924J GLY 3.9 0.4 - - - -
925J GLU* 3.0 34.1 + - - +
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Residues in contact with SER 922 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430J HIS* 5.9 0.2 - - - -
493J PRO* 4.6 4.2 - - - +
494J ALA* 3.3 37.7 - - - +
918J ILE 2.9 14.7 + - - -
919J ALA 2.7 19.9 + - - -
921J GLN* 1.3 76.9 - - - +
923J ILE* 1.3 58.4 + - - +
924J GLY 3.2 1.6 - - - -
925J GLU* 4.7 0.7 - - - -
926J PRO* 2.9 28.6 - - - +
1248J ILE* 3.5 7.2 - - - +
1252J HIS* 3.0 25.4 - - - -
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Residues in contact with ILE 923 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796J LEU* 4.2 13.3 - - + +
800J LEU* 4.7 5.6 - - + -
919J ALA 2.9 15.6 + - - +
920J ALA* 4.1 2.9 - - - +
922J SER* 1.3 78.2 + - - +
924J GLY* 1.3 59.7 + - - +
926J PRO* 4.4 0.2 - - - -
927J GLY* 4.8 0.2 - - - -
1141J VAL* 5.3 1.1 - - + -
1145J PHE* 3.8 27.1 - - + -
1241J TYR* 2.4 38.7 + - + +
1248J ILE* 4.6 6.3 - - + -
1252J HIS* 3.2 40.6 - - + +
1253J ILE* 3.3 26.0 - - + -
1256J ILE* 3.8 17.7 - - + -
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Residues in contact with GLY 924 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796J LEU* 4.1 15.1 - - - +
797J THR* 3.9 19.1 - - - -
920J ALA 2.8 16.6 + - - -
921J GLN 4.2 0.2 - - - -
923J ILE* 1.3 78.3 - - - +
925J GLU* 1.3 54.1 + - - +
926J PRO 3.3 0.7 - - - -
927J GLY* 2.4 36.7 + - - -
928J THR* 3.8 2.0 + - - +
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Residues in contact with GLU 925 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429J LEU* 3.5 36.0 - - + +
430J HIS* 3.1 38.6 + - + +
493J PRO* 6.0 1.2 - - - +
494J ALA* 4.5 9.1 - - + +
797J THR* 4.5 2.0 + - - +
921J GLN* 3.0 24.7 + - - +
922J SER* 4.7 1.6 - - - +
924J GLY* 1.3 71.5 - - - +
926J PRO* 1.3 76.5 - - + +
928J THR* 2.4 34.6 + - - -
929J GLN* 4.2 14.1 + - - +
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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