Contacts of the helix formed by residues 92 - 97 (chain I) in PDB entry 1HNX
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 TYR 92 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I VAL* 3.6 40.4 + - + +
58I ARG* 4.5 9.2 + - - -
59I PHE* 5.1 2.4 - + - -
85I LEU* 2.7 53.8 - - + +
86I VAL* 4.6 2.0 - - + -
88I TYR* 3.3 28.4 - + - -
89I ASN* 2.8 40.3 + - + +
91I ASP* 1.3 78.9 - - - +
93I ARG* 1.3 68.7 + - - +
95I LYS* 2.7 8.9 + - - +
96I LEU* 2.6 35.4 + - + +
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Residues in contact with ARG 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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1178A G 2.8 20.6 + - - +
1179A A 3.6 21.0 + - - -
86I VAL* 3.6 27.4 - - + +
90I PRO* 3.7 11.9 + - - +
92I TYR* 1.3 75.3 - - - +
94I ALA* 1.3 55.0 + - - +
95I LYS 2.4 15.1 + - - -
96I LEU* 2.6 18.6 + - - +
97I LYS* 2.7 62.5 + - + +
98I PRO* 3.3 2.1 - - - +
102I LEU* 3.8 15.8 - - + +
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Residues in contact with ALA 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I ASP* 3.8 15.6 + - - +
92I TYR 3.2 0.2 - - - -
93I ARG* 1.3 76.5 - - - +
95I LYS* 1.3 61.4 + - + +
97I LYS* 5.6 0.2 - - - -
98I PRO* 3.5 16.9 - - - +
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Residues in contact with LYS 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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52I ALA* 5.6 9.9 - - - +
53I VAL* 4.5 16.6 - - + -
91I ASP 5.5 0.7 - - - +
92I TYR* 2.7 8.6 + - - +
93I ARG 2.4 9.0 + - - -
94I ALA* 1.3 77.0 - - + +
96I LEU* 1.3 58.4 + - - +
98I PRO* 3.5 8.2 - - + +
99I LEU* 3.0 39.4 - - + +
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Residues in contact with LEU 96 (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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49I PRO 3.9 8.5 - - - +
52I ALA* 3.8 23.1 - - + -
53I VAL* 5.5 2.2 - - + +
82I ALA* 3.1 33.9 - - + +
85I LEU* 4.6 7.6 - - + -
86I VAL* 3.4 18.8 - - + -
92I TYR* 2.6 31.0 + - + +
93I ARG* 2.6 3.8 + - - -
95I LYS* 1.3 71.9 - - - +
97I LYS* 1.3 60.9 + - - +
99I LEU* 3.5 6.1 + - - +
100I GLY 3.4 11.4 + - - -
101I PHE* 3.6 38.1 + - + -
102I LEU* 4.3 8.7 - - + -
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Residues in contact with LYS 97 (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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1177A G 5.9 3.1 - - - +
1178A G 2.8 34.3 + - + +
1179A A 3.0 22.6 + - - -
93I ARG* 2.7 73.7 + - + +
96I LEU* 1.3 68.7 - - - +
98I PRO* 1.3 59.7 - - + +
99I LEU 2.9 6.1 - - - -
100I GLY* 2.5 29.6 + - - +
102I LEU* 3.2 29.6 - - + -
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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