Contacts of the helix formed by residues 107 - 117 (chain 3) in PDB entry 5U8T
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 ASP 107 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273 ARG* 3.2 30.8 + - - +
1033 LEU* 3.3 10.1 + - - +
1043 ARG* 4.9 0.2 - - - -
1063 PHE* 1.3 112.0 - - + +
1083 ARG* 1.3 57.3 + - - +
1093 SER* 4.7 7.9 - - - -
1103 PHE* 3.5 26.2 + - + +
1113 TRP* 2.8 30.3 + - - +
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Residues in contact with ARG 108 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043 ARG* 3.5 37.0 + - - +
1063 PHE 4.1 1.2 + - - -
1073 ASP* 1.3 71.5 - - - +
1093 SER* 1.3 60.9 + - - +
1103 PHE 3.1 0.2 - - - -
1113 TRP* 2.9 55.1 + - + +
1123 SER* 3.0 20.9 + - - -
89C LYS 3.3 14.5 + - - -
90C THR 3.3 21.8 + - - -
91C ASP* 4.6 2.6 + - - -
92C PRO* 5.2 4.6 - - - +
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Residues in contact with SER 109 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073 ASP* 4.7 10.3 - - - -
1083 ARG* 1.3 80.1 - - - +
1103 PHE* 1.3 56.1 + - - +
1123 SER* 4.1 10.1 + - - -
1133 GLY 4.6 0.2 + - - -
1213 PHE* 4.3 11.1 - - - -
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Residues in contact with PHE 110 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243 ARG* 4.4 22.0 - - + -
273 ARG* 4.9 10.1 - - + -
283 PHE* 3.8 35.7 - + + -
1033 LEU* 5.8 4.9 - - + -
1063 PHE* 5.8 4.3 - + - -
1073 ASP* 3.5 28.4 + - + +
1083 ARG 3.1 0.2 - - - -
1093 SER* 1.3 80.1 - - - +
1113 TRP* 1.3 66.7 + - - +
1123 SER 3.4 0.2 + - - -
1133 GLY 3.5 2.4 + - - -
1143 ILE* 3.1 46.8 + - + +
1213 PHE* 3.7 50.2 - + + -
1223 ILE* 6.0 0.2 - - - -
1253 ALA* 4.4 9.2 - - + -
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Residues in contact with TRP 111 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003 LEU* 3.1 58.8 - - + -
1033 LEU* 4.1 14.8 - - + +
1043 ARG* 3.6 19.7 - - + -
1073 ASP 2.8 19.8 + - - +
1083 ARG* 2.9 48.0 + - + +
1103 PHE* 1.3 76.6 - - - +
1123 SER* 1.3 90.6 + - - +
1143 ILE* 3.1 30.3 + - + +
1153 LEU* 3.9 24.5 + - + +
1603 SER 4.2 5.6 - - - -
1613 PHE* 5.1 0.7 - + - -
90C THR* 3.4 39.0 + - + -
91C ASP* 5.6 0.6 + - - -
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Residues in contact with SER 112 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083 ARG* 3.0 13.9 + - - -
1093 SER* 4.1 7.6 + - - -
1113 TRP* 1.3 92.8 - - - +
1133 GLY* 1.3 68.7 + - - +
1153 LEU* 3.0 12.8 + - - +
1163 VAL* 2.9 33.6 + - - +
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Residues in contact with GLY 113 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093 SER 4.6 0.2 + - - -
1103 PHE 3.5 2.6 + - - -
1113 TRP 3.3 1.0 - - - -
1123 SER* 1.3 80.4 + - - +
1143 ILE* 1.3 62.8 + - - +
1163 VAL* 3.3 14.6 - - - -
1173 GLU* 2.6 34.5 + - - -
1213 PHE* 3.3 26.1 - - - -
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Residues in contact with ILE 114 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003 LEU* 5.2 6.7 - - + -
1033 LEU* 4.3 22.4 - - + -
1103 PHE* 3.1 52.9 - - + +
1113 TRP* 3.1 23.8 + - + +
1133 GLY* 1.3 76.5 - - - +
1153 LEU* 1.3 63.4 + - + +
1183 PRO* 3.4 19.8 - - - +
1213 PHE* 3.4 11.0 - - + -
1223 ILE* 5.5 8.5 - - + +
1573 PHE* 4.3 28.5 - - + -
1793 LEU* 3.8 10.6 - - + +
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Residues in contact with LEU 115 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003 LEU* 4.0 11.2 - - + -
1113 TRP* 4.2 32.3 - - + +
1123 SER* 3.0 10.1 + - - +
1143 ILE* 1.3 77.5 - - + +
1163 VAL* 1.3 67.8 + - + +
1183 PRO* 3.5 2.1 - - - +
1613 PHE* 3.6 33.2 - - + -
1623 GLY* 6.0 1.1 - - - -
1633 ALA 5.8 0.7 - - - +
1643 HIS* 3.8 27.4 - - + +
1783 LYS* 3.1 4.9 - - - -
1793 LEU* 2.7 52.2 + - + +
91C ASP* 5.3 8.1 - - - +
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Residues in contact with VAL 116 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 SER* 2.9 30.0 + - - +
1133 GLY* 2.9 11.6 + - - -
1153 LEU* 1.3 78.3 - - + +
1173 GLU* 1.3 83.6 + - + +
1183 PRO* 3.4 0.2 - - - -
1643 HIS* 5.5 1.8 - - + -
1773 ASN 2.8 22.5 - - - +
1783 LYS* 3.2 35.6 - - - +
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Residues in contact with GLU 117 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133 GLY* 2.6 15.6 + - - +
1163 VAL* 1.3 94.3 - - + +
1183 PRO* 1.3 60.5 - - - +
1193 ALA* 3.1 4.7 - - + +
1203 TYR* 2.9 52.8 + - + +
1213 PHE* 3.4 12.3 + - + +
1773 ASN* 4.4 2.9 - - + +
2465 GLU 5.8 3.1 - - - +
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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