Contacts of the helix formed by residues 91 - 99 (chain F) in PDB entry 2AJQ
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 THR 91 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F VAL* 3.7 26.0 - - + -
58F PHE 3.2 3.4 + - - -
59F HIS* 2.5 41.6 + - - +
89F ILE* 4.1 0.4 - - + -
90F ASP* 1.3 72.3 - - - +
92F LEU* 1.3 56.1 + - - +
94F LEU* 4.3 3.8 - - + +
95F SER* 2.7 32.9 + - - -
178F THR* 4.1 19.7 - - + +
181F LEU* 3.9 11.7 - - - +
182F LEU* 4.1 22.2 - - + +
185F LEU* 3.9 8.2 - - + +
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F HIS* 3.5 18.4 - - + +
60F ASN* 3.4 37.2 - - + +
90F ASP* 3.0 13.1 + - - +
91F THR* 1.3 81.4 + - - +
93F VAL* 1.3 58.9 + - + +
95F SER* 3.7 1.3 - - - -
96F ARG* 3.1 58.5 + - - +
123F HIS* 3.5 39.3 - - + +
124F ALA* 5.4 0.4 - - - -
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Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F HIS* 4.5 2.2 - - + -
90F ASP* 2.9 35.1 + - + +
92F LEU* 1.3 78.5 - - + +
94F LEU* 1.3 67.2 + - + +
96F ARG* 3.3 8.4 + - - +
97F LEU* 3.1 20.8 + - - +
217F GLU* 3.7 40.9 - - + +
218F HIS* 4.1 14.1 - - + +
221F ALA* 3.8 22.7 - - + -
423F ASN* 5.9 0.5 - - - +
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Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ILE* 4.2 21.8 - - + -
90F ASP 3.0 10.3 + - - +
91F THR* 3.9 3.6 - - - +
93F VAL* 1.3 74.7 - - + +
95F SER* 1.3 59.2 + - - +
97F LEU* 3.0 16.1 + - + +
98F ILE* 2.8 39.7 + - + +
182F LEU* 4.4 13.9 - - + -
185F LEU* 3.7 25.1 - - + -
186F LEU* 5.0 1.1 - - + -
192F PHE* 4.0 24.9 - - + -
206F PHE* 5.2 1.1 - - + -
214F VAL* 3.5 31.4 - - + -
218F HIS* 3.7 15.3 - - + -
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Residues in contact with SER 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F THR 2.7 23.9 + - - -
92F LEU* 3.7 7.6 - - - -
94F LEU* 1.3 73.7 - - - +
96F ARG* 1.3 57.3 + - - +
99F HIS* 2.9 27.5 + - - +
123F HIS* 2.7 35.1 + - - -
128F TRP* 2.8 30.1 + - - -
181F LEU* 4.8 2.0 - - - -
185F LEU* 4.0 17.0 - - - +
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Residues in contact with ARG 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LEU* 3.1 48.4 + - - +
93F VAL* 3.8 5.2 - - - +
94F LEU 3.2 0.2 - - - -
95F SER* 1.3 78.9 - - - +
97F LEU* 1.3 61.3 + - - +
100F SER* 3.4 17.4 - - - -
123F HIS* 3.6 34.2 + - + +
421F ASN* 2.9 52.5 + - - +
422F PRO* 4.3 7.2 - - - +
423F ASN* 2.9 32.5 + - + +
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Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F VAL 3.1 11.4 + - - +
94F LEU* 3.0 17.6 + - + +
96F ARG* 1.3 79.2 - - - +
98F ILE* 1.3 67.1 + - + +
100F SER* 3.9 12.0 + - - -
191F TYR* 4.0 30.2 + - + -
213F ALA* 4.0 12.8 - - + +
214F VAL* 4.0 30.1 - - + +
217F GLU* 3.9 13.0 - - + -
423F ASN* 3.6 6.9 + - - +
599F ARG* 3.5 46.5 - - + +
600F LYS 5.2 2.1 - - - +
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F LEU* 2.8 25.9 + - + +
97F LEU* 1.3 78.2 - - + +
99F HIS* 1.3 77.3 + - + +
100F SER* 3.6 3.5 + - - -
185F LEU* 3.7 45.1 - - + +
188F ASP* 3.5 26.7 - - + +
191F TYR* 3.8 35.3 + - + -
192F PHE* 4.1 15.7 - - + -
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Residues in contact with HIS 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F SER 2.9 14.2 + - - +
98F ILE* 1.3 86.3 + - + +
100F SER* 1.3 56.7 + - - +
101F ASN 3.2 9.4 + - - +
102F LEU* 3.7 24.6 - - + +
105F THR* 5.6 7.5 + - + +
123F HIS* 3.0 20.7 + - - +
128F TRP* 3.3 36.2 - + + -
184F LYS* 3.5 30.4 + - - +
185F LEU* 3.7 26.4 - - + +
188F ASP* 5.8 0.7 - - - -
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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