Contacts of the helix formed by residues 1048 - 1061 (chain A) in PDB entry 5UAK
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 ARG1048 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A SER* 5.4 5.3 + - - -
188A LEU* 3.4 41.4 - - + +
1044A GLU* 3.3 15.8 + - - +
1045A SER* 3.4 24.0 + - - +
1046A GLU 3.1 0.4 - - - -
1047A GLY* 1.3 78.9 - - - +
1049A SER* 1.3 62.9 + - - +
1050A PRO 3.6 0.5 - - - -
1051A ILE* 3.7 12.8 + - - +
1052A PHE* 3.5 34.9 - - + -
1085A HIS* 4.4 11.6 + - - +
1089A TRP* 4.7 15.3 - - - -
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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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1045A SER 4.4 1.7 + - - -
1046A GLU* 3.1 16.0 + - - -
1048A ARG* 1.3 77.9 - - - +
1050A PRO* 1.4 65.7 - - - +
1052A PHE* 3.1 6.8 + - - +
1053A THR* 2.8 42.8 + - - +
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Residues in contact with PRO1050 (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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1046A GLU 3.5 6.7 - - - +
1047A GLY* 3.5 17.0 - - - +
1048A ARG 3.4 4.9 - - - -
1049A SER* 1.4 97.9 - - - +
1051A ILE* 1.3 55.3 + - + +
1053A THR* 3.1 7.9 + - - +
1054A HIS* 3.0 31.0 + - - +
1081A ALA* 4.4 17.6 - - + +
1084A LEU* 5.7 11.0 - - + -
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Residues in contact with ILE1051 (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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157A PHE* 6.4 0.9 - - + -
184A LEU* 5.3 10.1 - - + -
1047A GLY 4.6 5.8 - - - +
1048A ARG* 3.7 8.2 + - - +
1049A SER 3.2 0.6 - - - -
1050A PRO* 1.3 75.0 - - - +
1052A PHE* 1.3 62.9 + - + +
1054A HIS* 3.4 2.9 + - - +
1055A LEU* 2.8 42.1 + - + +
1078A PHE* 3.9 26.3 - - + -
1081A ALA* 3.4 40.8 - - + +
1082A LEU* 4.1 16.8 - - + +
1085A HIS* 4.0 24.9 - - + +
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Residues in contact with PHE1052 (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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181A VAL* 4.1 34.5 - - + -
184A LEU* 3.9 35.9 - - + -
185A SER* 4.1 21.1 - - - -
188A LEU* 5.4 4.9 - - + -
1048A ARG* 3.5 36.8 - - + +
1049A SER* 3.1 9.7 + - - +
1051A ILE* 1.3 83.3 - - + +
1053A THR* 1.3 60.6 + - + +
1055A LEU* 3.3 7.6 + - + +
1056A VAL* 2.8 40.7 + - + +
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Residues in contact with THR1053 (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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499A PRO* 5.4 3.6 - - - -
543A GLU* 5.2 3.9 - - + +
1049A SER* 2.8 38.4 + - - +
1050A PRO* 3.1 16.1 + - - +
1052A PHE* 1.3 73.0 - - + +
1054A HIS* 1.3 57.7 + - - +
1056A VAL* 4.0 6.0 - - - +
1057A THR* 3.0 32.7 + - - +
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Residues in contact with HIS1054 (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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161A TYR* 3.2 24.5 + - - -
499A PRO* 5.3 11.2 - - + -
1050A PRO 3.0 21.2 + - - +
1051A ILE* 3.7 4.5 - - - +
1053A THR* 1.3 75.9 + - - +
1055A LEU* 1.3 59.2 + - - +
1057A THR* 2.8 20.7 + - - -
1058A SER* 3.0 17.7 + - - -
1074A PHE* 3.7 33.1 + + - -
1077A LEU* 3.5 29.3 - - + +
1078A PHE* 3.6 28.8 - - + -
1081A ALA* 5.3 4.2 - - + +
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Residues in contact with LEU1055 (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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160A ILE* 5.2 9.0 - - + -
161A TYR* 4.2 23.6 - - + -
164A THR* 5.4 8.3 - - + +
180A LEU* 5.0 13.2 - - + -
181A VAL* 4.5 21.5 - - + -
184A LEU* 3.8 29.2 - - + -
1051A ILE* 2.8 23.3 + - + +
1052A PHE* 3.8 9.2 - - + +
1054A HIS* 1.3 73.2 + - - +
1056A VAL* 1.3 66.6 + - + +
1058A SER* 3.0 18.0 + - - +
1059A LEU* 3.6 14.3 + - + +
1078A PHE* 4.5 10.5 - - + -
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Residues in contact with VAL1056 (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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181A VAL* 5.1 15.0 - - + -
543A GLU* 4.4 22.9 - - + +
1052A PHE* 2.8 31.1 + - + +
1053A THR* 4.0 5.6 - - - +
1055A LEU* 1.3 73.5 - - + +
1057A THR* 1.3 67.1 + - - +
1059A LEU* 3.1 22.6 + - - +
1060A LYS* 3.4 15.5 + - + +
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Residues in contact with THR1057 (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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496A TRP* 3.1 31.0 - - + -
498A MET* 5.4 0.2 - - - -
499A PRO* 3.7 34.0 - - + +
543A GLU* 3.4 38.4 - - + -
1053A THR 3.0 15.2 + - - +
1054A HIS* 2.8 25.8 + - - -
1056A VAL* 1.3 75.0 - - - +
1058A SER* 1.3 56.2 + - - +
1060A LYS* 3.0 24.3 + - - +
1061A GLY 3.4 0.3 + - - -
1074A PHE* 5.8 0.7 - - - -
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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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161A TYR* 3.9 16.6 + - - -
165A LEU* 5.0 8.5 - - - +
496A TRP* 4.6 0.7 - - - -
1054A HIS 3.0 15.9 + - - -
1055A LEU* 3.0 22.2 + - - +
1057A THR* 1.3 77.2 + - - +
1059A LEU* 1.3 58.7 + - - +
1060A LYS 3.6 0.3 + - - -
1061A GLY 3.9 8.5 + - - +
1062A LEU* 3.9 14.6 + - - +
1065A LEU* 4.6 6.8 - - - +
1074A PHE* 3.8 36.1 - - - -
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Residues in contact with LEU1059 (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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164A THR* 4.9 15.7 - - - +
167A LEU* 6.6 0.2 - - + -
172A LEU* 4.9 11.8 - - + +
177A ILE* 4.0 38.1 - - + -
180A LEU* 6.1 6.3 - - + -
1055A LEU* 3.8 12.1 - - + +
1056A VAL* 3.1 14.8 + - - +
1058A SER* 1.3 79.1 + - - +
1060A LYS* 1.3 69.3 + - + +
1062A LEU* 3.7 31.0 - - + +
1063A TRP* 6.0 0.5 - - - -
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Residues in contact with LYS1060 (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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494A PHE* 6.1 5.3 - - - -
496A TRP* 4.1 13.9 - - + +
543A GLU* 4.8 17.3 - - + +
1056A VAL* 3.6 21.1 - - + +
1057A THR* 3.0 13.9 + - - +
1059A LEU* 1.3 82.6 - - + +
1061A GLY* 1.3 57.8 + - - +
1062A LEU* 3.2 5.1 + - - +
1063A TRP* 4.6 14.6 - - - -
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Residues in contact with GLY1061 (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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496A TRP* 3.7 26.6 + - - -
1057A THR 3.4 6.9 + - - -
1058A SER* 3.9 6.2 + - - +
1059A LEU 3.5 0.2 - - - -
1060A LYS* 1.3 75.6 - - - +
1062A LEU* 1.3 57.8 + - - -
1063A TRP* 3.6 1.1 - - - -
1064A THR* 2.8 28.5 + - - -
1065A LEU* 3.0 19.8 + - - +
1074A PHE* 5.7 1.0 - - - -
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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