Contacts of the helix formed by residues 102 - 107 (chain H) in PDB entry 1HNW
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 ARG 102 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79E GLU* 4.9 2.9 - - - +
100H ILE 3.9 0.9 + - - +
101H PRO* 1.3 71.2 - - - +
103H VAL* 1.3 67.6 + - - +
104H ARG 3.3 2.9 + - - -
105H ARG* 3.5 12.1 + - - +
106H GLY* 4.6 10.8 - - - +
121H ASP* 4.6 3.8 - - - +
125H ARG* 3.3 40.1 - - - +
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Residues in contact with VAL 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H PRO* 3.7 7.9 + - + +
102H ARG* 1.3 69.5 - - - +
104H ARG* 1.3 70.6 + - - +
106H GLY 2.9 12.6 + - - -
108H GLY 3.3 11.1 + - - +
109H ILE* 3.1 42.6 - - - +
110H ALA* 3.4 18.4 - - + -
121H ASP* 5.1 2.6 + - - +
136H GLU* 3.6 22.2 - - + +
138H TRP* 3.4 39.7 - - + -
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Residues in contact with ARG 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E HIS* 3.4 33.7 + - - +
79E GLU* 3.1 33.5 + - - -
80E ILE* 3.3 28.4 - - - +
81E GLU 5.4 0.4 - - - +
141E GLN* 5.3 6.9 + - - +
102H ARG 3.3 2.2 + - - -
103H VAL* 1.3 75.7 - - - +
105H ARG* 1.3 69.3 + - - +
107H LEU* 2.8 22.7 + - - +
108H GLY 3.7 11.4 - - - +
138H TRP* 2.7 78.7 + - + +
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Residues in contact with ARG 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A G 5.3 6.9 + - - -
76E ILE 6.0 0.2 - - - +
77E PRO 4.2 6.7 - - - +
78E HIS* 3.8 17.9 - - + +
79E GLU* 4.1 19.3 + - - +
92E LYS* 5.6 4.9 - - - +
93E PRO* 3.1 47.6 + - + +
94E ALA* 5.2 1.4 - - - +
102H ARG* 3.5 13.8 + - - +
103H VAL 3.3 1.2 + - - -
104H ARG* 1.3 74.8 - - - +
106H GLY* 1.3 55.8 + - - +
107H LEU* 3.3 11.6 + - - +
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Residues in contact with GLY 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E LYS* 5.7 1.5 - - - -
102H ARG* 4.3 10.1 + - - +
103H VAL 2.9 9.4 + - - -
104H ARG 2.9 0.2 + - - -
105H ARG* 1.3 75.1 - - - +
107H LEU* 1.3 63.0 + - - +
108H GLY 2.9 16.2 + - - +
109H ILE* 5.2 1.4 - - - +
122H ARG* 3.6 30.4 + - - -
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Residues in contact with LEU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E PRO* 4.1 7.9 - - + +
78E HIS* 3.5 18.8 - - + +
143E ARG 3.1 28.3 - - - +
144E THR* 4.3 0.4 - - - -
145E LYS* 4.0 38.8 - - + +
148E VAL* 3.7 25.9 - - + +
152E ARG* 2.5 35.3 + - - -
104H ARG* 2.8 25.3 + - + +
105H ARG 3.9 8.3 - - - +
106H GLY* 1.3 73.7 - - - +
108H GLY* 1.3 51.4 + - - +
109H ILE* 5.5 0.2 - - - -
138H TRP* 4.7 4.0 - - - +
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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