Contacts of the helix formed by residues 93 - 99 (chain N) in PDB entry 1T6V
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 93 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L TRP* 3.9 10.3 - - + -
73L ARG* 2.6 42.7 + - - -
37N TYR* 3.1 13.5 + - - -
48N SER* 4.7 2.0 - - - -
91N TYR* 3.2 19.2 + - + -
92N CYS* 1.3 74.8 - - - +
94N TYR* 1.3 68.5 + - - +
95N ALA* 2.9 31.0 + - - +
96N LEU* 2.8 25.9 + - + +
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Residues in contact with TYR 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N TYR* 3.3 31.2 - + + -
46N GLU* 2.7 61.8 + - + +
47N GLU 6.1 0.2 - - - -
48N SER* 5.3 0.2 + - - -
82N ARG* 2.8 46.0 + - - -
93N ASP* 1.3 75.0 + - - +
95N ALA* 1.3 60.4 + - - +
96N LEU 3.1 0.2 - - - -
97N CYS* 3.0 30.8 + - + +
98N SER* 4.6 3.4 + - - -
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Residues in contact with ALA 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L ARG* 3.6 30.4 + - - +
62L TRP* 3.7 18.4 - - + -
73L ARG* 4.6 1.8 - - - +
93N ASP* 2.9 16.3 + - - +
94N TYR* 1.3 76.4 - - - +
96N LEU* 1.3 62.6 + - - +
97N CYS 3.0 4.0 + - - -
98N SER* 3.3 18.1 + - - +
99N SER* 3.6 6.4 + - - -
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Residues in contact with LEU 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L TRP* 3.6 40.0 - - + -
37N TYR* 4.2 4.5 - - - +
85N LEU 4.1 15.5 - - - +
87N VAL* 4.0 29.4 - - + -
91N TYR* 3.7 24.9 - - + +
92N CYS* 4.1 2.0 - - - -
93N ASP 2.8 27.7 + - - +
95N ALA* 1.3 77.8 - - - +
97N CYS* 1.3 58.8 + - - +
99N SER* 2.9 35.2 + - - +
101N TYR* 4.9 2.7 - - + -
102N ALA* 3.8 18.0 - - + +
104N CYS* 5.4 0.9 - - - -
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Residues in contact with CYS 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N TYR* 4.0 17.0 - - - -
82N ARG* 3.9 16.4 - - - -
93N ASP 5.1 0.2 - - - -
94N TYR* 3.0 25.1 + - + +
95N ALA 3.0 1.0 - - - -
96N LEU* 1.3 78.3 - - - +
98N SER* 1.3 60.0 + - - +
99N SER 3.4 2.4 + - - +
102N ALA 4.9 3.2 - - - +
103N GLU* 5.2 1.0 - - - -
104N CYS* 2.0 58.3 + - + +
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Residues in contact with SER 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77M ASN* 4.9 17.6 + - - +
94N TYR* 5.4 3.3 + - - -
95N ALA* 3.3 12.0 + - - -
96N LEU 3.1 0.4 - - - -
97N CYS* 1.3 78.1 - - - +
99N SER* 1.3 60.6 + - - +
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Residues in contact with SER 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L TRP* 3.8 24.5 - - - -
112L ARG* 5.1 0.5 + - - -
95N ALA 3.6 7.2 + - - -
96N LEU* 2.9 23.9 + - - +
97N CYS 4.7 1.9 - - - +
98N SER* 1.3 81.6 - - - +
100N ARG* 1.3 61.4 + - - +
101N TYR* 3.0 24.3 + - - +
102N ALA 3.5 15.6 + - - +
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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