Contacts of the helix formed by residues 109 - 122 (chain P) in PDB entry 1HH2
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 109 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27P LEU* 5.8 0.2 - - - +
30P ALA* 5.1 6.4 + - - +
31P LEU* 4.4 8.5 - - - +
34P ALA* 3.9 22.5 - - + +
106P ALA* 3.1 19.8 + - + +
107P ALA 4.2 1.4 + - - -
108P GLN* 1.3 92.6 - - - +
110P ALA* 1.3 64.9 + - - +
111P LYS 2.8 7.4 + - - -
112P GLN* 2.9 22.6 + - + +
113P VAL* 3.0 15.9 + - - +
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Residues in contact with ALA 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P LEU* 6.4 0.4 - - + -
7P GLU* 4.1 14.6 - - - +
27P LEU* 3.2 38.1 - - + +
31P LEU* 5.4 5.8 - - + +
56P ILE* 6.2 1.6 - - + -
107P ALA 3.2 14.0 + - - +
108P GLN* 3.0 1.4 + - - +
109P THR* 1.3 81.5 + - - +
111P LYS* 1.3 49.7 + - - +
113P VAL* 3.6 1.8 - - - +
114P LEU* 2.6 46.8 + - + +
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Residues in contact with LYS 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P GLN* 2.8 37.2 + - + +
109P THR 2.8 0.6 + - - -
110P ALA* 1.3 74.3 - - - +
112P GLN* 1.3 97.6 + - - +
114P LEU* 2.5 34.2 + - - +
115P ILE* 2.6 38.1 + - + +
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Residues in contact with GLN 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P THR* 2.9 14.6 + - + +
111P LYS* 1.3 103.5 - - - +
113P VAL* 1.3 58.5 + - + +
115P ILE* 3.2 7.0 + - - +
116P GLN* 2.7 55.2 + - - +
119P ARG* 5.3 7.6 + - - +
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Residues in contact with VAL 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P VAL* 4.4 5.6 - - + +
26P ILE* 3.7 28.7 - - + +
27P LEU* 3.3 37.7 - - + +
30P ALA* 3.6 25.6 - - + -
109P THR* 3.0 12.5 + - - +
110P ALA* 3.6 0.7 - - - +
111P LYS 3.0 0.6 - - - -
112P GLN* 1.3 82.5 - - + +
114P LEU* 1.3 64.6 + - - +
116P GLN* 3.3 8.6 + - - +
117P ARG* 3.1 25.7 + - + +
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Residues in contact with LEU 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P GLU* 5.2 4.9 - - - +
10P ASP* 4.5 28.9 - - + +
11P GLN* 5.7 8.3 - - - +
18P ILE* 5.2 9.0 - - + +
23P VAL* 3.3 31.9 - - + -
27P LEU* 4.9 5.2 - - + -
110P ALA* 2.6 35.1 + - + +
111P LYS* 2.5 15.8 + - - +
113P VAL* 1.3 73.0 - - - +
115P ILE* 1.3 62.8 - - + +
117P ARG* 3.3 12.1 + - - +
118P ILE* 3.2 19.1 + - - +
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Residues in contact with ILE 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P LYS* 2.6 46.8 + - + +
112P GLN* 3.7 7.6 - - - +
114P LEU* 1.3 68.7 - - + +
116P GLN* 1.3 57.5 + - - +
117P ARG 3.0 1.8 - - - -
118P ILE* 2.4 44.8 + - + +
119P ARG* 2.9 24.4 + - + -
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Residues in contact with GLN 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P GLN* 2.7 45.9 + - - +
113P VAL* 3.6 8.6 - - - +
115P ILE* 1.3 73.5 - - - +
117P ARG* 1.3 59.8 + - - +
118P ILE 3.0 0.7 + - - -
119P ARG* 3.5 20.3 + - + +
120P GLU* 3.4 27.3 + - + +
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Residues in contact with ARG 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P ILE* 4.7 25.3 - - + +
19P SER 4.9 7.2 + - - +
22P GLU* 3.4 39.4 - - + +
23P VAL* 5.1 15.3 - - + -
26P ILE* 5.8 7.9 - - + -
113P VAL* 3.1 14.3 + - + +
114P LEU* 3.6 11.7 - - - +
115P ILE 3.0 1.2 - - - -
116P GLN* 1.3 77.2 - - - +
118P ILE* 1.3 60.6 + - - +
120P GLU* 3.8 8.2 + - + +
121P LEU* 2.8 52.3 + - - +
125P LYS* 5.4 6.4 - - - +
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Residues in contact with ILE 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LYS* 3.3 40.7 - - + +
18P ILE* 3.2 36.1 - - + -
114P LEU 3.2 16.4 - - - +
115P ILE* 2.4 33.6 + - + +
117P ARG* 1.3 72.7 - - - +
119P ARG* 1.3 64.0 + - + +
120P GLU 3.0 1.6 - - - -
121P LEU* 3.1 8.6 + - + +
122P GLU* 3.0 23.7 + - - +
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Residues in contact with ARG 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P GLN* 5.3 9.2 + - - +
115P ILE* 2.9 28.7 + - + +
116P GLN* 3.5 20.7 + - - +
118P ILE* 1.3 79.2 - - + +
120P GLU* 1.3 60.6 + - + +
122P GLU* 3.1 26.0 + - - +
123P LYS* 3.7 13.0 - - - +
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Residues in contact with GLU 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P GLN* 3.4 21.7 + - + +
117P ARG* 3.9 11.9 - - + +
118P ILE 3.0 1.0 - - - -
119P ARG* 1.3 77.2 - - + +
121P LEU* 1.3 63.8 + - + +
122P GLU 3.1 1.6 - - - -
123P LYS* 3.1 45.7 + - - +
125P LYS* 2.8 49.3 - - + +
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Residues in contact with LEU 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LYS* 5.8 6.5 - - + -
17P GLY 6.2 0.2 - - - +
18P ILE* 6.1 4.5 - - + -
117P ARG* 2.8 49.4 - - - +
118P ILE* 3.1 10.1 + - + +
120P GLU* 1.3 72.1 - - + +
122P GLU* 1.3 56.9 + - - +
123P LYS 2.8 6.1 - - - -
124P GLU* 2.8 28.3 + - - +
125P LYS* 3.3 33.2 - - + +
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Residues in contact with GLU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P ILE* 3.0 16.1 + - + +
119P ARG* 3.1 20.9 - - - +
120P GLU 3.1 0.4 - - - -
121P LEU* 1.3 76.5 - - - +
123P LYS* 1.3 58.5 + - + +
124P GLU* 3.3 4.0 + - - +
129P LYS* 2.8 29.5 + - - +
156P LYS* 2.8 36.5 + - + +
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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