Contacts of the helix formed by residues 89 - 97 (chain N) in PDB entry 6T9L
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 ALA 89 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K MET 4.5 4.7 - - - +
167K SER* 3.9 32.3 - - - +
168K GLN* 5.2 4.7 - - + +
172K ASN* 6.2 0.4 - - - +
85N LEU* 4.3 5.9 - - + +
86N ALA* 3.2 12.0 + - + +
88N THR* 1.3 82.9 + - - +
90N ILE* 1.3 61.7 + - - +
91N VAL 3.5 1.6 - - - -
92N ASP* 4.1 14.0 - - + +
93N HIS* 3.6 20.3 + - - +
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Residues in contact with ILE 90 (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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111K ASP* 5.2 1.3 - - - +
114K LEU* 5.6 7.0 - - + -
121K VAL* 4.3 20.0 - - + -
125K THR* 4.0 22.4 - - + -
76N ARG* 3.9 27.6 - - + -
85N LEU* 4.6 15.9 - - + +
86N ALA 3.2 15.9 - - - +
87N LEU* 3.7 36.7 + - + +
88N THR 3.5 2.4 - - - -
89N ALA* 1.3 75.8 - - - +
91N VAL* 1.3 67.3 + - - +
92N ASP 3.4 0.3 + - - -
93N HIS* 3.5 8.1 + - - +
94N LEU* 3.3 26.8 + - + +
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Residues in contact with VAL 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K LEU* 4.8 20.1 - - + +
117K TYR* 4.9 30.5 - - + -
120K ASP* 6.1 0.4 - - - +
88N THR 4.7 9.0 - - - +
90N ILE* 1.3 81.6 - - + +
92N ASP* 1.3 79.5 + - - +
93N HIS 3.5 0.2 + - - -
94N LEU* 3.5 11.3 + - - +
95N GLU* 3.5 35.1 + - + +
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Residues in contact with ASP 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172K ASN* 5.6 7.4 - - - +
88N THR 4.6 10.6 - - - +
89N ALA* 4.0 11.6 + - + +
90N ILE 3.3 1.0 - - - -
91N VAL* 1.3 94.1 - - - +
93N HIS* 1.3 60.3 + - - +
94N LEU 3.6 0.2 + - - -
95N GLU* 3.7 7.0 + - - +
96N ASN* 3.1 25.1 - - - +
97N HIS* 3.4 7.9 + - + +
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Residues in contact with HIS 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168K GLN* 5.3 5.8 - - + +
172K ASN* 5.7 0.4 + - - -
81N CYS* 2.8 16.4 - - + -
83N LYS* 3.8 20.8 - - + +
85N LEU* 3.5 38.8 - - + +
89N ALA 3.6 9.0 + - - +
90N ILE 3.5 1.9 + - - +
91N VAL 3.3 0.4 - - - -
92N ASP* 1.3 79.6 - - - +
94N LEU* 1.3 60.8 + - + +
97N HIS* 3.1 40.9 + - + +
98N CYS* 2.7 33.8 + - - -
701N ZN 2.3 36.9 - - - -
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Residues in contact with LEU 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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120K ASP* 3.6 26.5 - - + +
121K VAL* 6.1 0.4 - - + -
124K LYS* 3.7 48.8 - - + +
125K THR* 4.4 8.1 - - + -
78N CYS* 4.2 9.0 - - + -
85N LEU* 5.3 2.0 - - + -
90N ILE* 3.3 32.7 + - + +
91N VAL* 3.5 7.4 + - - +
92N ASP 3.4 0.8 - - - -
93N HIS* 1.3 80.7 - - + +
95N GLU* 1.3 62.4 + - + +
98N CYS* 4.0 10.3 - - + +
701N ZN 4.2 19.1 - - - -
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Residues in contact with GLU 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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91N VAL* 3.5 31.4 + - + +
92N ASP* 3.7 5.3 + - - +
93N HIS 3.2 0.6 - - - -
94N LEU* 1.3 82.6 - - + +
96N ASN* 1.3 69.8 + - - +
97N HIS 3.7 0.7 - - - -
98N CYS 5.1 0.4 - - - -
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Residues in contact with ASN 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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92N ASP* 3.1 8.8 - - - +
95N GLU* 1.3 82.4 + - + +
97N HIS* 1.3 98.6 + - - +
98N CYS 3.9 0.2 - - - -
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Residues in contact with HIS 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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171K SER 5.3 2.5 - - - -
172K ASN* 3.0 47.6 + - + +
83N LYS* 5.9 0.2 - - - -
92N ASP* 3.4 12.6 + - + -
93N HIS* 3.1 38.7 + - - +
96N ASN* 1.3 113.9 + - - +
98N CYS* 1.3 64.9 + - - +
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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