Contacts of the helix formed by residues 1044 - 1055 (chain A) in PDB entry 3Q71
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 GLY1044 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800A AR6 3.5 29.1 + - - -
1041A LEU 4.8 1.0 + - - -
1043A ARG* 1.3 79.3 - - - +
1045A PRO* 1.3 69.3 - - - +
1046A LEU 3.3 2.4 + - - -
1047A SER* 3.4 6.0 + - - -
1048A LYS* 2.9 31.9 + - - +
1136A ASN* 3.9 1.8 - - - -
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Residues in contact with PRO1045 (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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800A AR6 3.3 43.5 - - + +
1043A ARG 4.5 1.6 - - - +
1044A GLY* 1.3 83.7 - - - +
1046A LEU* 1.3 59.5 + - - +
1048A LYS* 3.9 7.7 - - + +
1049A SER* 3.0 28.6 + - - -
1136A ASN* 4.1 10.1 - - - +
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Residues in contact with LEU1046 (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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800A AR6 2.9 73.5 + - + +
1023A VAL* 3.8 19.8 - - + +
1032A VAL 4.6 1.1 - - - +
1033A ASN* 4.0 13.7 - - - +
1034A SER* 4.2 12.1 - - - +
1045A PRO* 1.3 71.9 - - - +
1047A SER* 1.3 64.3 + - - +
1049A SER* 3.2 7.3 + - - -
1050A LEU* 3.1 18.4 + - + +
1130A PRO* 3.6 35.9 - - + -
1132A ILE* 4.0 18.6 - - + -
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Residues in contact with SER1047 (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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800A AR6 4.4 3.1 + - - -
1033A ASN* 3.0 35.3 + - - +
1034A SER 4.0 12.3 - - - -
1035A VAL* 4.3 1.1 - - - +
1036A PRO* 6.1 0.7 - - - -
1040A VAL 5.4 0.7 - - - -
1041A LEU* 2.9 36.3 + - - +
1044A GLY* 3.4 10.4 + - - -
1046A LEU* 1.3 80.0 - - - +
1048A LYS* 1.3 57.3 + - - +
1050A LEU* 3.1 4.7 + - - +
1051A LEU* 2.8 26.5 + - - +
1058A LEU* 5.5 0.2 - - - +
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Residues in contact with LYS1048 (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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1041A LEU 3.2 9.8 + - - +
1042A SER* 3.9 30.4 + - - +
1043A ARG 5.7 0.4 - - - -
1044A GLY 2.9 20.9 + - - +
1045A PRO* 3.9 7.6 - - + +
1047A SER* 1.3 77.0 - - - +
1049A SER* 1.3 62.4 + - - +
1051A LEU* 3.2 5.8 + - + +
1052A GLU* 2.9 51.4 + - + +
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Residues in contact with SER1049 (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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800A AR6 2.9 33.8 + - - -
1023A VAL* 4.2 1.8 - - - -
1024A GLN* 3.8 19.6 + - - +
1045A PRO 3.0 17.4 + - - -
1046A LEU 3.3 8.1 - - - -
1048A LYS* 1.3 76.4 - - - +
1050A LEU* 1.3 61.4 + - - +
1052A GLU* 3.6 8.7 + - - +
1053A LYS* 3.3 23.7 + - - +
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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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1023A VAL* 3.9 39.9 - - + +
1024A GLN* 5.3 0.4 - - - -
1031A VAL* 4.3 9.4 - - + -
1032A VAL 4.7 0.2 - - - +
1033A ASN* 3.4 40.6 - - + +
1046A LEU* 3.1 7.0 + - + +
1047A SER* 3.1 10.3 + - - +
1049A SER* 1.3 76.9 - - - +
1051A LEU* 1.3 58.6 + - - +
1053A LYS* 3.9 1.0 - - - +
1054A ALA* 2.9 33.6 + - - +
1058A LEU* 4.2 10.5 - - + -
1084A LEU* 3.3 39.0 - - + -
1089A VAL* 4.3 12.3 - - + -
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Residues in contact with LEU1051 (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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1041A LEU* 4.2 20.6 - - + -
1042A SER* 4.0 27.8 - - - +
1047A SER 2.8 18.6 + - - +
1048A LYS* 3.2 7.8 + - + +
1050A LEU* 1.3 74.0 - - - +
1052A GLU* 1.3 59.4 + - + +
1055A GLY* 2.9 46.8 + - - +
1056A PRO* 4.3 7.0 - - + -
1058A LEU* 4.2 6.4 - - + +
1059A GLN* 4.1 32.1 - - + +
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Residues in contact with GLU1052 (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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1048A LYS* 2.9 49.7 + - + +
1049A SER* 4.0 7.3 - - - +
1051A LEU* 1.3 80.8 - - + +
1053A LYS* 1.3 61.9 + - - +
1055A GLY* 3.9 5.9 + - - -
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Residues in contact with LYS1053 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1024A GLN* 3.5 39.3 - - + +
1025A ASN* 4.8 8.9 + - - +
1049A SER 3.3 7.5 + - - +
1050A LEU 4.0 0.2 - - - +
1052A GLU* 1.3 80.0 - - - +
1054A ALA* 1.3 62.1 + - - +
1055A GLY* 4.7 0.2 - - - -
1083A ASN* 3.1 40.4 + - - +
1084A LEU* 3.4 23.1 - - + -
1085A ASP* 4.2 11.8 + - - -
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Residues in contact with ALA1054 (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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1050A LEU 2.9 19.5 + - - +
1051A LEU 4.1 0.2 - - - +
1053A LYS* 1.3 77.6 - - - +
1055A GLY* 1.3 58.8 + - - +
1057A GLU* 4.2 2.1 - - - +
1058A LEU* 3.9 23.3 - - + -
1081A SER 3.7 9.0 - - - +
1082A TRP* 3.3 10.8 - - + +
1083A ASN* 3.1 31.9 + - - +
1084A LEU* 3.7 24.0 - - + -
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Residues in contact with GLY1055 (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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1051A LEU* 2.9 19.8 + - - +
1052A GLU 3.9 4.0 + - - -
1053A LYS 3.4 2.6 - - - -
1054A ALA* 1.3 78.9 - - - +
1056A PRO* 1.4 73.8 - - - +
1057A GLU* 3.0 11.0 + - - -
1058A LEU* 3.0 18.5 + - - +
1083A ASN* 5.3 3.8 - - - -
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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