Contacts of the helix formed by residues 113 - 118 (chain B) in PDB entry 3TKY
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 PRO 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.8 10.7 - - + +
112B ALA* 1.3 85.6 - - + +
114B VAL* 1.3 57.0 + - - +
116B LYS* 2.8 32.3 + - + +
58D GLY 6.2 0.9 - - - +
59D TYR* 4.3 14.1 - - + -
96D THR* 3.9 25.1 - - + -
98D ARG* 3.7 27.6 - - - +
108D LEU* 4.9 9.0 - - + -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.5 28.0 - - - +
24A PHE* 3.7 16.8 - - + -
25A ALA* 3.6 23.3 - - + +
28A LEU* 4.4 3.1 - - + -
91B SER 4.1 0.2 - - - +
92B VAL* 3.7 33.4 - - + +
112B ALA 3.1 1.1 + - - +
113B PRO* 1.3 76.9 - - - +
115B CYS* 1.3 61.3 + - - +
116B LYS 3.0 0.2 - - - -
117B PHE* 2.9 21.1 + - - +
118B LEU* 3.5 20.2 + - + +
98D ARG* 3.2 20.3 - - - +
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Residues in contact with CYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.4 15.3 - - - -
92B VAL* 3.1 29.2 - - - -
93B VAL* 4.8 3.1 - - - -
111B LEU* 3.5 42.6 - - + -
112B ALA 2.8 21.6 + - - +
114B VAL* 1.3 73.7 - - - +
116B LYS* 1.3 64.0 + - - +
117B PHE 3.0 1.0 + - - -
118B LEU* 3.6 9.2 - - - +
119B THR* 2.8 35.9 + - + -
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP* 3.3 37.8 + - - +
21A ALA* 5.5 1.3 - - + -
112B ALA 4.1 0.4 + - - -
113B PRO* 2.8 16.6 + - + +
115B CYS* 1.3 80.7 - - - +
117B PHE* 1.3 88.2 + - + +
118B LEU 3.5 0.2 - - - -
119B THR* 3.9 1.4 - - - +
121B ASN* 2.4 34.5 + - - +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP* 3.1 34.5 - - + -
21A ALA* 3.7 14.8 - - + -
22A ASN* 3.6 29.6 - - + -
25A ALA* 4.2 6.7 - - + -
114B VAL 2.9 8.7 + - - +
116B LYS* 1.3 111.0 - - + +
118B LEU* 1.3 57.7 + - - +
119B THR 3.6 1.8 - - - -
126B SER* 4.1 3.8 - - - +
127B LEU* 2.7 50.9 + - + +
189B ILE* 3.6 32.8 - - + -
357B PHE* 4.1 12.8 - + - -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 4.0 20.6 - - + +
28A LEU* 4.6 4.0 - - + -
38B LEU* 4.5 20.2 - - + -
42B ILE* 4.8 7.0 - - + +
47B LEU* 4.0 29.2 - - + +
48B GLU* 4.6 1.7 - - - +
92B VAL* 4.7 3.1 - - + -
114B VAL* 3.8 34.5 - - + +
115B CYS* 3.2 5.4 + - - -
117B PHE* 1.3 83.7 - - - +
119B THR* 1.3 65.9 - - - +
126B SER* 3.6 8.7 - - - -
127B LEU* 4.6 4.7 - - + +
128B ALA* 3.7 28.1 - - - +
131B LEU* 4.6 18.4 - - + -
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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