Contacts of the helix formed by residues 1047 - 1058 (chain A) in PDB entry 2PDA
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 GLN1047 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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694A GLN* 5.6 0.2 - - - +
796A LEU* 4.1 20.2 - - + +
1044A TYR 4.9 2.2 + - - -
1045A SER* 3.1 22.0 + - - +
1046A LYS* 1.3 95.8 + - - +
1048A GLN* 1.3 58.0 + - - +
1050A LEU* 3.3 9.4 + - - +
1051A LYS* 2.9 27.4 + - - +
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Residues in contact with GLN1048 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039A THR 3.3 16.3 - - - +
1040A VAL* 3.4 22.6 - - - +
1045A SER* 3.2 26.3 + - - +
1047A GLN* 1.3 79.1 - - - +
1049A PHE* 1.3 64.3 + - - +
1051A LYS* 3.5 11.6 + - + +
1052A VAL* 3.1 25.2 + - - +
1098A LEU* 3.7 22.3 - - + +
1099A PHE 4.3 1.6 - - - +
1100A ARG* 4.8 4.7 - - - +
1116A ASP* 3.1 35.4 - - + +
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Residues in contact with PHE1049 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A PHE* 4.4 5.2 - + - -
820A TYR* 3.3 42.4 - + + -
823A VAL* 3.4 26.9 - - + -
824A ILE* 4.3 1.3 - - + -
987A PHE* 4.0 17.5 - + - -
1040A VAL* 3.8 22.9 - - + -
1041A SER 5.3 1.6 - - - +
1042A MET* 3.5 32.5 - - + -
1045A SER 3.5 12.7 + - - +
1046A LYS* 3.7 9.0 - - - +
1047A GLN 3.2 0.2 - - - -
1048A GLN* 1.3 85.2 - - - +
1050A LEU* 1.3 58.5 + - - +
1052A VAL* 2.8 20.4 + - + +
1053A LEU* 2.8 36.5 + - + +
1065A VAL* 5.1 0.9 - - + -
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Residues in contact with LEU1050 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A PHE* 4.1 12.1 - - + -
794A ASP* 3.5 25.1 - - + +
795A SER* 3.6 2.0 - - - -
796A LEU* 3.1 40.8 - - + +
799A SER* 4.1 3.8 - - - +
823A VAL* 4.0 26.7 - - + -
827A LEU* 4.2 25.3 - - + +
1046A LYS 3.1 18.2 + - - +
1047A GLN* 3.3 6.9 + - - +
1049A PHE* 1.3 79.3 - - + +
1051A LYS* 1.3 55.0 + - - +
1053A LEU* 3.8 5.5 - - + +
1054A LYS* 2.9 30.8 + - - +
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Residues in contact with LYS1051 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794A ASP* 5.6 0.7 - - - -
1047A GLN 2.9 17.2 + - - +
1048A GLN* 3.7 13.0 - - + +
1049A PHE 3.1 0.2 - - - -
1050A LEU* 1.3 76.0 - - - +
1052A VAL* 1.3 59.4 + - + +
1054A LYS* 4.1 5.2 - - + +
1055A GLU* 3.0 54.0 + - + +
1100A ARG* 3.1 37.1 - - - +
1114A GLN* 3.8 5.1 + - - -
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Residues in contact with VAL1052 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036A TYR* 4.0 5.6 - - + +
1038A ALA* 3.8 13.0 - - + -
1040A VAL* 3.8 24.5 - - + -
1048A GLN* 3.1 20.1 + - - +
1049A PHE* 2.8 8.8 + - + +
1051A LYS* 1.3 76.5 - - - +
1053A LEU* 1.3 61.9 + - + +
1055A GLU* 3.8 0.2 - - - +
1056A ALA* 2.7 35.5 + - - +
1065A VAL* 3.9 29.6 - - + -
1100A ARG* 3.5 34.1 - - + -
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Residues in contact with LEU1053 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823A VAL* 3.7 24.7 - - + +
824A ILE* 3.6 36.1 - - + -
827A LEU* 4.2 13.0 - - + -
828A PHE* 3.8 11.8 - - + -
958A TRP* 3.8 27.3 - - + -
987A PHE* 5.0 5.4 - - + -
1049A PHE* 2.8 34.8 + - + +
1050A LEU* 3.8 8.1 - - + +
1052A VAL* 1.3 83.3 - - + +
1054A LYS* 1.3 63.7 + - - +
1056A ALA* 4.0 1.1 - - - +
1057A GLU* 3.1 25.6 + - - +
1065A VAL* 5.2 2.7 - - + -
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Residues in contact with LYS1054 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794A ASP* 3.9 25.8 - - + +
827A LEU* 4.9 2.2 - - + +
828A PHE* 4.4 7.8 - - - -
1050A LEU 2.9 18.3 + - - +
1051A LYS* 4.3 5.2 - - + +
1053A LEU* 1.3 77.4 - - - +
1055A GLU* 1.3 66.7 + - + +
1057A GLU* 4.3 1.4 - - - +
1058A SER* 2.8 35.7 + - - +
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Residues in contact with GLU1055 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036A TYR* 2.7 40.2 + - + +
1051A LYS* 3.0 52.2 + - + +
1052A VAL 3.2 1.6 + - - +
1054A LYS* 1.3 83.3 - - + +
1056A ALA* 1.3 63.9 + - - +
1058A SER* 3.2 6.5 + - - -
1059A PHE* 3.2 6.2 + - - +
1100A ARG* 3.3 18.6 + - - -
1102A ASP* 4.0 11.2 - - - +
1104A ARG* 3.1 31.1 + - - +
1114A GLN* 4.8 0.6 + - - -
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Residues in contact with ALA1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958A TRP* 5.2 6.5 - - + -
985A ASN* 3.8 1.8 - - + +
1036A TYR* 3.9 18.1 - - + -
1052A VAL 2.7 21.3 + - - +
1053A LEU* 4.0 2.9 - - - +
1055A GLU* 1.3 70.0 - - - +
1057A GLU* 1.3 63.8 + - - +
1058A SER 3.3 0.7 + - - -
1059A PHE* 3.5 6.1 + - - +
1063A SER* 2.7 36.8 + - - -
1065A VAL* 3.8 22.4 - - + -
1238A CA 2.8 8.1 - - - -
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Residues in contact with GLU1057 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A PHE* 3.3 43.2 - - + -
831A ARG* 3.1 27.2 + - - -
920A PRO* 5.1 2.1 - - - +
954A LYS* 4.6 6.8 + - - -
956A SER* 2.7 38.4 + - - +
958A TRP* 3.8 3.1 - - + -
983A ASP* 4.2 6.8 - - - +
985A ASN* 3.2 20.3 + - - +
1053A LEU 3.1 5.1 + - - +
1054A LYS 4.3 1.3 - - - +
1056A ALA* 1.3 79.1 - - - +
1058A SER* 1.3 59.5 + - - +
1059A PHE 4.1 0.7 - - - +
1238A CA 3.3 10.7 - - - -
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Residues in contact with SER1058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054A LYS* 2.8 33.4 + - - +
1055A GLU* 3.2 2.6 + - - -
1057A GLU* 1.3 79.5 - - - +
1059A PHE* 1.3 64.8 + - - +
1060A PRO* 3.1 10.7 - - - +
1104A ARG* 2.7 27.5 + - - -
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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