Contacts of the helix formed by residues 85 - 97 (chain I) in PDB entry 3TKR
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 PHE 85 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A VAL* 4.0 18.4 - - + -
219A ILE* 3.2 24.9 - - + +
221A PRO* 3.5 38.8 - - + -
222A ASP* 3.5 26.7 - - - -
223A PRO* 4.0 2.0 - - + -
226A LYS* 3.9 24.9 - - + -
230A PHE* 3.7 4.4 - - - -
117E PHE* 3.6 35.0 - + - -
83I PHE 4.7 1.8 - - - -
84I THR* 1.3 98.2 + - + +
86I VAL* 1.3 66.1 + - - +
87I CYS 3.3 0.4 - - - -
88I PRO* 3.2 15.2 - - - +
89I THR* 3.6 2.8 - - - +
163I ARG* 5.8 0.2 - - - +
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Residues in contact with VAL 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 3.6 31.9 - - + -
208A CYS 3.5 20.9 - - - +
209A PRO 4.6 0.2 - - - -
219A ILE* 4.2 3.4 - - + -
85I PHE* 1.3 76.2 - - - +
87I CYS* 1.3 64.1 + - - +
89I THR* 2.6 29.9 + - - +
90I GLU* 3.1 10.5 + - + +
163I ARG* 3.4 31.0 - - - +
182I LEU 4.3 2.9 - - - +
183I PRO 4.0 6.3 - - - +
185I GLY* 3.5 30.7 - - - +
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Residues in contact with CYS 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I TYR* 3.7 19.4 - - + +
80I PRO* 3.4 22.4 - - - -
81I LEU 3.6 15.0 - - - +
84I THR* 3.4 21.1 - - - +
86I VAL* 1.3 75.8 - - - +
88I PRO* 1.3 70.6 - - + +
90I GLU* 3.1 8.0 + - - +
91I ILE* 3.1 25.3 + - - +
122I TRP* 4.1 4.0 - - + -
163I ARG* 3.2 28.7 - - - +
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Residues in contact with PRO 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PHE* 3.6 19.3 - - + -
84I THR 3.4 22.7 - - - +
85I PHE 3.2 18.8 - - - +
87I CYS* 1.3 94.3 - - + +
89I THR* 1.3 54.9 + - - +
91I ILE* 3.8 0.6 - - + +
92I ILE* 2.8 38.7 + - + +
122I TRP* 3.5 23.1 - - + -
130I GLY 4.0 9.9 - - - +
131I GLY 4.5 4.0 - - - +
132I LEU* 3.8 18.6 - - + -
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Residues in contact with THR 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PRO* 3.4 8.0 - - + +
210A ALA* 3.0 27.6 + - - +
219A ILE* 3.7 14.4 - - + -
229A TYR* 3.5 28.9 - - + +
230A PHE* 4.3 5.6 - - + -
85I PHE 3.6 17.3 - - - +
86I VAL 2.6 16.2 + - - -
88I PRO* 1.3 76.9 - - - +
90I GLU* 1.3 55.8 + - - +
92I ILE* 4.0 7.5 - - + +
93I ALA* 2.9 32.2 + - - +
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Residues in contact with GLU 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA* 3.9 18.4 - - + -
77I PHE* 4.4 11.9 - - + -
79I TYR* 4.4 1.3 - - + +
86I VAL* 3.7 21.7 - - + +
87I CYS* 3.1 8.3 + - - +
89I THR* 1.3 75.8 + - - +
91I ILE* 1.3 65.4 + - - +
93I ALA* 3.3 0.4 + - - -
94I PHE* 3.0 39.3 + - + -
163I ARG* 2.8 22.3 + - - -
185I GLY* 3.4 2.8 - - - -
186I ARG* 2.8 66.1 + - + +
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Residues in contact with ILE 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I PHE* 4.2 15.7 - - + -
79I TYR* 3.6 34.5 - - + +
87I CYS 3.1 16.5 + - - +
88I PRO 3.8 3.4 - - - +
90I GLU* 1.3 75.4 - - - +
92I ILE* 1.3 58.9 + - + +
95I GLY* 3.0 27.2 + - - -
110I ALA* 4.5 2.0 - - + -
122I TRP* 3.4 34.8 - - + -
132I LEU* 4.0 18.8 - - + -
135I ILE* 4.0 25.2 - - + +
137I ILE* 4.0 12.9 - - + +
139I LEU* 4.2 4.5 - - + -
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Residues in contact with ILE 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PHE* 5.6 5.6 - - + -
233A LEU* 6.2 4.9 - - + -
234A ASN* 6.2 0.7 - - - +
88I PRO* 2.8 27.6 + - + +
89I THR* 4.0 6.1 - - - +
91I ILE* 1.3 75.5 - - + +
93I ALA* 1.3 63.8 + - - +
95I GLY* 5.0 0.7 - - - -
96I ASP* 2.8 53.5 + - - +
127I ARG* 3.6 41.5 - - + +
131I GLY 3.9 17.7 - - - +
132I LEU* 4.1 12.3 - - + +
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Residues in contact with ALA 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ALA* 3.7 17.5 - - + +
89I THR 2.9 20.5 + - - +
90I GLU 3.3 2.2 + - - +
92I ILE* 1.3 81.0 - - - +
94I PHE* 1.3 61.7 + - - +
96I ASP* 4.3 2.4 - - - +
97I ARG* 3.5 26.5 + - - +
188I VAL* 3.7 22.1 - - + +
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Residues in contact with PHE 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ALA* 6.0 1.1 - - + -
75I VAL* 4.3 5.2 - - + -
77I PHE* 3.8 23.6 - + + -
90I GLU* 3.0 33.6 + - + +
91I ILE 4.2 1.6 - - - +
93I ALA* 1.3 75.5 - - - +
95I GLY* 1.3 66.5 + - - +
97I ARG 3.1 5.2 + - - -
98I LEU* 3.1 21.8 + - - +
101I PHE* 3.7 36.0 - + - -
108I VAL* 4.1 22.8 - - + +
137I ILE* 4.8 2.7 - - + -
165I LEU* 3.7 17.0 - - + -
186I ARG* 4.9 12.6 - - + -
187I SER 4.3 2.7 - - - -
188I VAL* 4.0 25.1 - - + -
191I THR* 3.6 30.1 - - + -
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Residues in contact with GLY 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I ILE 3.0 18.1 + - - -
92I ILE* 5.0 0.4 - - - -
94I PHE* 1.3 78.6 - - - +
96I ASP* 1.3 62.9 + - - +
97I ARG 3.1 1.2 + - - -
98I LEU* 3.1 18.6 + - - +
135I ILE* 5.9 2.5 - - - -
136I ARG* 4.9 12.0 + - - +
137I ILE* 4.1 25.0 - - - +
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Residues in contact with ASP 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I ILE* 2.8 31.2 + - + +
93I ALA* 4.3 3.4 - - - +
95I GLY* 1.3 71.5 - - - +
97I ARG* 1.3 63.7 + - + +
98I LEU 3.5 0.2 - - - -
127I ARG* 2.8 45.6 + - - -
134I PRO 4.6 1.0 - - - +
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Residues in contact with ARG 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I ALA* 3.5 19.0 + - - +
94I PHE 3.1 6.1 + - - +
95I GLY 3.0 1.0 - - - -
96I ASP* 1.3 83.9 - - + +
98I LEU* 1.3 64.1 + - - +
99I GLU* 3.1 3.4 - - - -
100I GLU* 2.9 62.9 + - + +
101I PHE* 3.7 6.1 - - + -
188I VAL* 3.7 27.4 - - + +
189I ASP* 2.8 43.8 + - - -
192I LEU* 3.5 9.3 - - - +
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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