Contacts of the helix formed by residues 109 - 125 (chain I) in PDB entry 2HPC
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 109 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H ARG* 2.8 34.8 - - - +
105I SER 3.1 15.3 + - - +
106I SER 5.1 0.2 - - - -
107I ILE 2.5 4.4 + - - -
108I ARG* 1.3 74.4 - - - +
110I LEU* 1.3 58.2 + - + +
112I GLU* 2.5 47.1 + - + +
113I ILE* 3.2 28.4 - - + +
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Residues in contact with LEU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G LEU* 5.2 0.7 - - - -
165H LEU* 4.4 4.9 - - + -
166H ARG* 6.3 0.2 - - - +
168H LEU* 3.4 33.0 - - + +
169H ARG* 3.4 76.1 - - + +
172H LEU* 4.4 6.2 - - + +
106I SER* 3.0 28.0 - - - +
107I ILE* 2.6 7.9 + - - +
109I TYR* 1.3 67.8 - - + +
111I GLN* 1.3 51.0 + - - +
112I GLU 2.4 18.8 + - - -
113I ILE* 2.9 10.4 + - + +
114I TYR* 2.9 26.2 + - - +
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Residues in contact with GLN 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G HIS 5.3 3.0 + - - -
136G LEU* 3.6 44.5 - - + +
168H LEU* 5.2 0.2 - - - +
107I ILE* 2.8 26.9 + - + +
108I ARG* 3.8 20.2 - - - +
109I TYR 3.4 0.4 - - - -
110I LEU* 1.3 69.3 - - - +
112I GLU* 1.3 57.8 + - - +
114I TYR* 4.5 5.4 - - - -
115I ASN* 4.2 9.5 - - - +
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Residues in contact with GLU 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I ARG 4.0 4.9 - - - +
109I TYR* 2.5 27.3 + - + +
110I LEU 2.4 15.6 + - - -
111I GLN* 1.3 69.5 - - - +
113I ILE* 1.3 68.9 + - + +
114I TYR 2.9 4.5 - - - -
115I ASN* 2.9 25.9 + - - +
116I SER* 3.2 11.6 + - - -
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Residues in contact with ILE 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H ARG* 5.5 2.9 - - - +
172H LEU* 3.1 29.2 - - + -
173H GLU* 3.9 10.8 - - - +
176H ARG* 4.0 22.0 - - - +
109I TYR* 3.2 53.2 - - + +
110I LEU* 2.9 7.8 + - + +
112I GLU* 1.3 83.6 - - + +
114I TYR* 1.3 57.1 - - - +
116I SER* 2.6 26.2 + - - +
117I ASN* 2.9 14.7 + - - -
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Residues in contact with TYR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G LEU* 4.6 11.0 - - + -
139G ASN* 2.6 50.8 + - + +
140G VAL* 3.1 45.5 - - + -
142G ALA* 4.9 1.6 - - - +
143G GLN* 3.8 18.0 + - - +
172H LEU* 3.9 16.7 - - + +
110I LEU 2.9 16.2 + - - +
111I GLN* 4.5 7.2 - - - -
112I GLU 2.9 0.2 - - - -
113I ILE* 1.3 76.9 - - - +
115I ASN* 1.3 60.4 + - + +
116I SER 2.6 16.4 + - - -
117I ASN 3.2 8.7 + - - -
118I ASN* 3.2 38.3 + - - +
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Residues in contact with ASN 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I GLN 4.2 11.7 - - - +
112I GLU* 2.9 22.1 + - - +
114I TYR* 1.3 84.4 - - + +
116I SER* 1.3 56.4 + - - +
118I ASN* 5.1 4.7 - - - +
119I GLN* 3.3 28.9 + - - +
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Residues in contact with SER 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ARG* 4.6 2.1 - - - -
112I GLU* 3.2 9.1 + - - -
113I ILE* 2.6 27.0 + - - +
114I TYR 2.6 7.3 + - - -
115I ASN* 1.3 75.2 - - - +
117I ASN* 1.3 65.5 + - - -
119I GLN* 2.7 15.3 + - - +
120I LYS* 2.6 55.2 + - - +
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Residues in contact with ASN 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G GLN* 3.4 25.0 + - + +
172H LEU* 4.3 5.9 - - - +
175H LEU* 4.4 0.2 - - - +
176H ARG* 3.3 29.6 - - - +
179H ILE* 2.9 37.3 - - + +
113I ILE 2.9 11.8 + - - +
116I SER* 1.3 82.9 + - - +
118I ASN* 1.3 53.4 + - - +
119I GLN 2.4 17.0 + - - -
120I LYS* 2.6 24.1 + - - +
121I ILE* 2.7 22.6 + - + +
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Residues in contact with ASN 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G ALA 5.8 1.4 + - - -
143G GLN* 2.5 39.0 + - - +
146G ASP* 4.7 7.1 - - - +
114I TYR* 3.2 41.6 + - + +
115I ASN* 4.9 5.2 - - - +
116I SER 3.4 0.2 - - - -
117I ASN* 1.3 77.4 - - - +
119I GLN* 1.3 56.3 + - - +
121I ILE* 4.2 15.1 - - - +
122I VAL* 3.5 17.0 - - - +
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Residues in contact with GLN 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I ASN* 3.3 26.4 + - - +
116I SER* 2.7 17.8 + - - +
117I ASN 2.4 15.8 + - - -
118I ASN* 1.3 68.7 - - - +
120I LYS* 1.3 65.6 + - + +
121I ILE 3.0 1.1 - - - -
122I VAL* 3.0 25.6 + - + +
123I ASN* 3.4 8.5 + - - +
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Residues in contact with LYS 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ARG* 5.8 6.5 - - + +
179H ILE* 5.2 10.3 - - + -
180H GLN* 5.0 15.0 - - - +
116I SER* 2.6 39.8 + - - +
117I ASN* 2.6 12.1 + - - +
119I GLN* 1.3 75.2 - - + +
121I ILE* 1.3 52.3 + - - +
123I ASN* 2.8 37.2 + - - +
124I LEU* 2.9 24.0 - - + +
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Residues in contact with ILE 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G GLN* 6.5 0.2 - - + -
146G ASP* 4.2 15.3 - - - +
147G MET* 3.5 36.6 - - + -
150G LEU* 3.7 21.3 - - + -
179H ILE* 3.6 18.8 - - + -
117I ASN* 2.7 21.1 + - + +
118I ASN* 4.2 14.8 - - - +
120I LYS* 1.3 73.8 - - - +
122I VAL* 1.3 63.6 + - + +
123I ASN 2.8 4.5 - - - -
124I LEU* 2.8 26.0 + - + +
125I LYS* 2.8 30.3 + - - +
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Residues in contact with VAL 122 (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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118I ASN 3.5 17.0 - - - +
119I GLN* 3.0 17.4 + - + +
121I ILE* 1.3 81.2 - - + +
123I ASN* 1.3 61.9 + - - +
125I LYS* 3.7 18.8 + - + +
126I GLU* 4.5 6.1 - - - +
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Residues in contact with ASN 123 (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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119I GLN* 3.4 8.4 + - - +
120I LYS* 2.8 39.9 + - - +
122I VAL* 1.3 78.7 - - - +
124I LEU* 1.3 62.6 + - + +
125I LYS 3.1 1.8 - - - -
126I GLU* 3.2 8.3 + - - +
127I LYS* 2.8 53.4 + - + +
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Residues in contact with LEU 124 (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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147G MET* 5.5 0.9 - - + -
150G LEU* 4.2 28.8 - - + +
154G ILE* 5.2 3.1 - - + -
179H ILE* 4.9 9.2 - - + +
180H GLN* 6.0 0.2 - - - +
182H LEU 4.6 7.9 - - - +
183H GLU* 4.0 39.0 - - + +
186H VAL* 6.3 0.7 - - + -
120I LYS* 2.9 26.9 - - + +
121I ILE* 2.8 18.6 + - + +
123I ASN* 1.3 73.0 - - + +
125I LYS* 1.3 59.1 + - - +
126I GLU 2.7 12.2 + - - -
127I LYS* 3.2 13.9 + - + +
128I VAL* 3.0 38.2 - - + +
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Residues in contact with LYS 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ASP* 3.9 14.8 + - - -
150G LEU* 3.5 38.7 - - + +
121I ILE* 2.8 33.7 + - - +
122I VAL* 3.9 13.0 - - + +
123I ASN 3.1 0.8 - - - -
124I LEU* 1.3 76.8 - - - +
126I GLU* 1.3 69.8 + - - +
129I ALA* 4.4 7.3 - - - +
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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