Contacts of the helix formed by residues 82 - 90 (chain A) in PDB entry 1TW8
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 SER 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PHE* 2.8 12.2 + - - +
81A ASN* 1.3 82.3 - - - +
83A PRO* 1.3 71.1 - - - +
85A LEU* 3.5 16.5 + - - +
86A LEU* 3.1 23.9 + - - +
160A GLU* 2.7 27.5 + - - -
163A LEU* 3.0 21.6 - - - +
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Residues in contact with PRO 83 (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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81A ASN 4.8 0.4 - - - -
82A SER* 1.3 82.7 - - - +
84A THR* 1.3 51.0 + - - +
86A LEU* 3.0 12.6 + - + +
87A PHE* 2.8 34.6 + - - +
154A LYS* 4.7 6.4 + - + -
158A ASN* 3.0 39.3 - - - +
160A GLU* 3.5 15.7 - - - +
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Residues in contact with THR 84 (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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83A PRO* 1.3 71.1 - - - +
85A LEU* 1.3 62.3 + - - +
86A LEU 2.8 10.1 + - - -
87A PHE* 2.9 15.0 + - + +
88A LEU* 3.0 13.3 + - + +
151A THR* 3.6 41.5 - - + +
154A LYS* 2.8 32.8 + - + +
155A MET* 3.8 5.0 + - + -
160A GLU* 2.6 26.2 + - - -
163A LEU* 5.5 0.7 - - - -
164A PHE* 3.8 19.3 - - + -
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Residues in contact with LEU 85 (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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59A TYR* 6.2 0.2 - - + -
80A PHE* 4.0 14.9 - - + +
82A SER* 3.5 23.1 + - - +
83A PRO 3.5 0.2 - - - -
84A THR* 1.3 80.3 - - - +
86A LEU* 1.3 59.2 + - - +
88A LEU* 3.9 9.0 - - + +
89A LEU* 3.3 47.6 + - + +
123A TYR* 3.4 57.7 - - + +
125A LEU* 4.9 5.2 - - + -
163A LEU* 3.8 13.6 - - + +
164A PHE* 4.8 14.8 - - + -
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Residues in contact with LEU 86 (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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77A TYR* 3.5 44.0 - - + +
80A PHE* 3.8 22.4 - - + -
82A SER 3.1 19.0 + - - +
83A PRO* 3.0 9.6 + - + +
84A THR 2.9 0.8 - - - -
85A LEU* 1.3 77.1 - - - +
87A PHE* 1.3 63.8 + - + +
88A LEU 3.0 4.7 - - - -
90A SER* 2.8 55.2 + - - +
13E G 4.0 33.4 - - - +
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Residues in contact with PHE 87 (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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83A PRO 2.8 11.3 + - - +
84A THR* 2.9 8.7 + - - +
86A LEU* 1.3 82.9 - - + +
88A LEU* 1.3 63.5 + - + +
90A SER 5.0 0.2 + - - -
112A THR* 5.2 0.9 + - - -
147A LYS* 3.6 26.4 - - + -
150A GLN* 3.3 45.8 - - + -
151A THR* 3.4 32.5 - - + -
154A LYS* 3.5 28.9 - - + +
13E G 4.8 14.9 - - - +
6F T 5.4 1.3 - - - -
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Residues in contact with LEU 88 (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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56A GLN* 3.8 3.8 + - - -
84A THR* 3.0 16.9 + - + +
85A LEU* 4.2 8.1 - - + +
86A LEU 3.0 0.8 - - - -
87A PHE* 1.3 83.4 - - + +
89A LEU* 1.3 69.1 + - + +
112A THR* 2.9 47.4 + - + -
125A LEU* 4.2 14.4 - - + -
143A ILE* 5.6 3.1 - - + -
147A LYS* 4.2 14.4 - - + -
151A THR* 3.4 45.5 - - + +
164A PHE* 3.9 26.0 - - + -
166A ILE* 5.5 2.9 - - + -
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Residues in contact with LEU 89 (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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56A GLN* 3.6 34.5 + - + +
59A TYR* 4.9 7.4 - - + -
60A LEU* 3.5 29.0 - - + +
80A PHE* 4.1 14.8 - - + -
85A LEU* 3.3 44.7 + - + +
86A LEU 3.1 1.4 + - - -
88A LEU* 1.3 90.7 - - + +
90A SER* 1.3 68.9 + - - +
116A LEU* 4.0 34.8 - - + -
123A TYR* 4.7 4.3 - - + -
125A LEU* 4.5 11.0 - - + -
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Residues in contact with SER 90 (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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56A GLN* 5.0 1.7 + - - -
60A LEU* 5.2 0.7 - - - -
77A TYR* 3.6 14.8 - - - -
80A PHE* 4.3 12.4 - - - -
86A LEU* 2.8 48.5 + - - +
87A PHE 4.8 1.0 + - - -
88A LEU 3.9 0.4 - - - -
89A LEU* 1.3 80.9 - - - +
91A ARG* 1.3 72.0 + - - +
111A ASP* 5.2 0.3 - - - +
13E G 3.3 27.6 - - - -
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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