Contacts of the helix formed by residues 794 - 805 (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 GLY 794 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1273I MET* 5.4 15.1 - - - +
1276I TRP* 5.2 2.3 - - - -
429J LEU* 4.9 4.7 - - - -
792J ASN* 3.1 1.5 - - - +
793J SER* 1.3 81.8 - - - +
795J TYR* 1.3 56.8 + - - -
796J LEU 3.7 0.4 - - - -
797J THR* 4.1 12.3 - - - -
798J ARG* 3.3 34.5 + - - +
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Residues in contact with TYR 795 (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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792J ASN* 3.0 59.1 + - + -
793J SER 3.7 0.4 - - - -
794J GLY* 1.3 76.3 - - - +
796J LEU* 1.3 79.1 + - + +
798J ARG* 3.3 8.7 + - - +
799J ARG* 3.0 51.1 + - - +
1138J LEU* 3.5 36.4 + - + +
1139J PRO* 3.6 26.3 - - + +
1142J ALA* 4.8 9.0 - - + +
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Residues in contact with LEU 796 (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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793J SER 5.4 0.4 + - - -
795J TYR* 1.3 99.3 - - + +
797J THR* 1.3 61.6 + - - +
799J ARG* 4.3 7.0 - - - +
800J LEU* 2.9 58.6 + - + +
923J ILE* 4.2 11.7 - - + +
924J GLY* 4.1 22.0 - - - +
1138J LEU* 5.0 15.5 - - + +
1141J VAL* 4.5 12.6 - - + -
1142J ALA* 3.4 43.3 - - + +
1145J PHE* 5.4 0.9 - - + -
1241J TYR* 5.4 0.2 - - - +
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Residues in contact with THR 797 (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* 6.1 2.0 - - + -
1276I TRP* 4.2 13.9 - - + -
429J LEU* 4.5 17.8 - - + +
793J SER 4.1 13.7 + - - -
794J GLY* 4.1 10.9 - - - -
795J TYR 3.3 0.6 - - - +
796J LEU* 1.3 81.0 - - - +
798J ARG* 1.3 61.2 + - - +
800J LEU* 3.8 4.0 - - - +
801J VAL* 2.9 31.8 + - + +
920J ALA 4.2 14.8 - - - +
921J GLN* 4.3 20.9 - - + -
924J GLY* 3.9 18.9 - - - -
925J GLU 5.3 1.1 - - - +
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Residues in contact with ARG 798 (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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1272I GLU* 4.5 21.2 - - - +
1273I MET* 4.8 11.1 - - - -
1276I TRP* 3.4 23.4 - - + -
339J ARG* 3.0 41.8 - - - +
794J GLY 3.3 27.3 + - - +
795J TYR* 3.3 9.3 + - - +
796J LEU 3.2 0.2 - - - -
797J THR* 1.3 79.8 - - - +
799J ARG* 1.3 61.4 + - + +
800J LEU 3.1 0.2 - - - -
801J VAL 3.3 0.7 + - - -
802J ASP* 2.9 45.5 + - + +
1325J PHE* 6.1 1.1 - - - -
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Residues in contact with ARG 799 (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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795J TYR* 3.0 45.4 + - - +
796J LEU* 3.7 6.4 - - - +
798J ARG* 1.3 79.7 - - + +
800J LEU* 1.3 62.7 + - + +
802J ASP* 4.3 6.1 - - + +
803J VAL* 3.9 14.1 + - - +
1142J ALA* 3.2 38.4 + - - +
1146J GLU* 5.2 4.2 + - - +
1309J ILE* 4.0 22.2 - - + +
1310J THR* 4.1 34.7 - - - +
1313J SER* 5.7 0.9 - - - -
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Residues in contact with LEU 800 (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* 2.9 56.1 + - + +
797J THR* 3.8 4.7 - - - +
799J ARG* 1.3 81.8 - - + +
801J VAL* 1.3 64.7 + - - +
802J ASP 3.3 0.2 - - - -
803J VAL* 3.0 20.1 + - - +
804J ALA* 3.3 9.4 + - - +
920J ALA* 3.9 19.5 - - + +
923J ILE* 4.7 9.4 - - + -
1145J PHE* 4.9 10.5 - - + -
1256J ILE* 3.3 47.2 - - + +
1309J ILE* 4.0 21.3 - - + -
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Residues in contact with VAL 801 (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* 3.6 51.4 - - + +
797J THR* 2.9 26.2 + - + +
798J ARG 3.9 2.9 - - - +
800J LEU* 1.3 76.8 - - - +
802J ASP* 1.3 60.5 + - - +
803J VAL 3.0 0.3 + - - -
805J GLN* 2.8 52.3 + - + +
916J GLY 5.7 0.2 - - - -
917J VAL* 4.2 12.6 - - + +
920J ALA* 3.3 23.1 - - + -
921J GLN* 4.8 3.4 - - + -
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Residues in contact with ASP 802 (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* 4.0 8.8 - - - -
798J ARG* 2.9 34.2 + - + +
799J ARG* 4.3 5.1 - - + -
800J LEU 3.3 0.4 - - - -
801J VAL* 1.3 83.8 - - - +
803J VAL* 1.3 58.8 + - - +
805J GLN* 4.8 5.4 - - - -
1313J SER* 2.8 20.9 + - - +
1325J PHE* 3.1 47.1 - - + +
1348J LYS* 3.9 19.7 + - + +
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Residues in contact with VAL 803 (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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799J ARG 3.9 9.6 + - - +
800J LEU* 3.0 29.1 - - + +
802J ASP* 1.3 80.1 - - - +
804J ALA* 1.3 64.1 + - + +
805J GLN 3.5 1.4 + - - -
806J ASP* 4.8 2.6 + - - +
1256J ILE* 4.6 2.2 - - + -
1259J GLN* 3.3 21.0 + - + -
1262J ARG* 2.8 30.9 + - - +
1309J ILE* 3.7 35.2 - - + +
1312J ALA* 4.1 10.3 - - + -
1313J SER* 3.8 23.1 - - - +
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Residues in contact with ALA 804 (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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800J LEU 3.3 3.7 + - - +
801J VAL* 3.8 1.3 - - - -
803J VAL* 1.3 77.8 - - + +
805J GLN* 1.3 63.7 + - - +
806J ASP 3.2 2.6 + - - -
807J LEU* 3.6 8.0 + - + +
916J GLY* 3.2 32.0 - - - +
1255J VAL* 4.2 5.4 - - + +
1256J ILE* 3.6 28.5 - - + -
1259J GLN* 3.3 28.3 - - + +
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Residues in contact with GLN 805 (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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1272I GLU* 5.1 0.4 + - - -
1276I TRP* 3.7 18.4 - - - +
1279I GLU* 2.8 35.7 + - - +
801J VAL* 2.8 25.8 + - + +
802J ASP* 4.7 3.4 - - - +
803J VAL 3.5 1.8 - - - -
804J ALA* 1.3 79.7 - - - +
806J ASP* 1.3 60.0 + - - +
807J LEU 3.1 9.7 + - - +
914J ALA* 5.7 0.9 - - - +
917J VAL* 3.9 23.0 + - + +
1347J LEU* 3.4 24.8 + - + +
1348J LYS* 3.1 44.7 - - - +
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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