Contacts of the helix formed by residues 1003 - 1010 (chain C) in PDB entry 4TU6
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 ASP1003 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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999C ARG 3.4 12.3 + - - +
1000C LEU 3.2 14.3 + - - +
1001C ALA 4.4 2.4 - - - +
1002C ILE* 1.3 78.3 - - - +
1004C LYS* 1.3 68.9 + - - +
1005C ARG* 2.7 54.4 + - - +
1006C PHE* 2.9 30.8 + - + +
1007C ARG* 3.7 3.6 + - - -
1084C THR* 5.6 1.0 - - - +
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Residues in contact with LYS1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002C ILE 3.5 4.4 + - - -
1003C ASP* 1.3 74.2 + - - +
1005C ARG* 1.3 62.8 + - + +
1006C PHE 3.2 1.2 + - - -
1007C ARG* 3.3 19.3 + - - +
1077C ARG* 5.6 2.3 + - - -
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Residues in contact with ARG1005 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003C ASP* 2.7 32.4 + - - +
1004C LYS* 1.3 78.6 - - + +
1006C PHE* 1.3 88.8 + - + +
1007C ARG 3.4 0.7 - - - -
1008C VAL* 5.0 2.1 + - - +
1009C PHE* 4.5 1.2 - - - -
1077C ARG* 3.4 48.4 + - + +
1080C ALA* 3.9 21.0 - - - +
1084C THR* 4.1 12.7 + - - +
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Residues in contact with PHE1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000C LEU* 3.4 39.5 - - + +
1003C ASP* 2.9 28.4 + - + -
1005C ARG* 1.3 109.9 - - + +
1007C ARG* 1.3 66.5 + - - +
1008C VAL 3.1 3.4 - - - -
1009C PHE* 2.9 30.1 + + + +
1010C THR* 3.6 8.7 + - - +
1031C LEU* 4.6 3.8 - - + -
1077C ARG* 3.3 26.9 - - - -
1080C ALA* 3.7 12.8 - - + -
1081C LEU* 3.3 42.4 - - + -
1084C THR* 4.0 3.6 - - + -
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Residues in contact with ARG1007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001C ALA 5.4 1.3 - - - -
1003C ASP 3.7 3.9 + - - -
1004C LYS* 3.3 17.0 + - - +
1005C ARG 3.4 1.2 - - - -
1006C PHE* 1.3 75.2 - - - +
1008C VAL* 1.3 62.0 + - - +
1009C PHE 3.1 0.2 + - - -
1010C THR* 2.8 31.4 + - - +
1011C LYS* 4.5 0.9 + - - +
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Residues in contact with VAL1008 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005C ARG 5.0 3.3 + - - +
1006C PHE 3.0 1.4 + - - -
1007C ARG* 1.3 79.4 - - - +
1009C PHE* 1.3 93.7 + - + +
1010C THR 3.4 0.4 + - - -
1011C LYS 4.0 11.0 + - - +
1013C VAL* 5.8 3.6 - - - +
1074C ILE* 4.6 24.7 - - + -
1077C ARG* 5.8 8.3 - - - +
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Residues in contact with PHE1009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C PHE* 2.9 25.1 + + + +
1008C VAL* 1.3 99.8 - - + +
1010C THR* 1.3 58.8 + - - +
1011C LYS 3.5 2.5 - - - -
1030C ASP* 3.2 10.2 - - - +
1031C LEU* 2.7 29.9 + - + +
1056C ILE* 3.9 27.4 - - + -
1060C ALA* 4.1 20.4 - - + -
1074C ILE* 3.9 10.5 - - + -
1077C ARG* 3.8 17.0 - - + -
1078C ALA* 3.6 39.5 - - + -
1081C LEU* 3.9 16.8 - - + -
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Residues in contact with THR1010 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001C ALA* 3.5 31.2 - - + +
1006C PHE 3.7 14.6 - - - +
1007C ARG* 2.8 22.2 + - - +
1009C PHE* 1.3 79.2 - - - +
1011C LYS* 1.3 62.9 + - - +
1030C ASP* 3.0 12.5 - - - +
1031C LEU* 3.9 20.4 - - + -
1032C SER* 3.1 18.9 + - - -
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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