Contacts of the helix formed by residues 111 - 129 (chain A) in PDB entry 5HH0
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 GLY 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.3 10.5 - - - +
110A HIS* 1.3 78.9 - - - +
112A ILE* 1.3 60.9 + - - +
114A SER* 3.5 5.6 + - - -
115A LEU* 3.2 22.3 + - - +
201A COA 2.8 37.9 + - - -
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA* 5.4 1.8 - - + -
10A LEU* 4.2 17.5 - - + -
13A VAL* 4.2 16.8 - - + -
57A ALA* 3.7 26.9 - - + -
64A VAL* 3.9 22.4 - - + -
65A GLY* 4.7 3.1 - - - -
103A VAL* 3.7 17.7 - - + -
107A PHE* 3.8 32.3 - - + +
110A HIS* 4.5 8.0 - - + +
111A GLY* 1.3 74.7 - - - +
113A GLY* 1.3 65.8 + - - +
115A LEU* 3.2 7.8 + - + +
116A LEU* 3.0 25.4 + - + +
201A COA 3.9 7.8 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.5 4.4 - - - +
103A VAL* 4.1 8.1 - - - -
111A GLY 3.4 0.2 - - - -
112A ILE* 1.3 76.2 - - - +
114A SER* 1.3 63.5 + - - +
116A LEU* 3.3 8.3 + - - +
117A LEU* 3.0 22.9 + - - +
149A PHE* 3.7 11.8 - - - -
201A COA 3.0 34.7 + - - -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY* 3.8 6.2 - - - -
112A ILE 3.3 0.2 - - - -
113A GLY* 1.3 75.8 - - - +
115A LEU* 1.3 58.7 + - - +
117A LEU* 3.3 4.0 + - - +
118A GLU* 2.9 37.0 + - - +
149A PHE* 3.7 6.1 - - - -
153A ARG* 3.1 32.9 + - - +
201A COA 2.6 23.5 + - - -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.4 14.4 - - + -
13A VAL* 4.3 18.6 - - + +
15A LEU* 4.0 33.7 - - + -
57A ALA* 5.6 1.3 - - + -
111A GLY 3.2 12.0 + - - +
112A ILE* 3.5 9.9 - - - +
114A SER* 1.3 80.2 - - - +
116A LEU* 1.3 61.6 + - - +
118A GLU* 3.4 7.8 + - + +
119A SER* 2.9 36.1 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 6.3 - - + -
55A LEU* 3.9 38.1 - - + +
57A ALA* 4.0 19.7 - - + +
65A GLY 4.0 1.3 - - - -
66A MET 3.7 28.7 - - - +
67A ILE* 3.9 14.8 - - + +
101A LEU* 3.9 19.1 - - + -
102A GLY 4.3 3.6 - - - +
103A VAL* 4.4 1.6 - - + -
112A ILE* 3.0 33.1 + - + +
113A GLY 3.7 4.9 - - - +
114A SER 3.3 0.2 - - - -
115A LEU* 1.3 75.3 - - + +
117A LEU* 1.3 63.9 + - - +
119A SER* 3.3 6.3 + - - -
120A LEU* 3.1 20.4 + - - +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 4.2 10.5 - - + +
98A ILE* 4.4 17.5 - - + -
101A LEU* 5.0 3.6 - - + +
113A GLY 3.0 16.8 + - - +
114A SER* 3.6 5.2 - - - +
116A LEU* 1.3 77.0 - - - +
118A GLU* 1.3 65.4 + - - +
120A LEU* 3.2 10.8 + - + +
121A LYS* 3.1 38.9 + - + +
135A ILE* 5.5 2.0 - - + -
149A PHE* 4.3 11.0 - - + -
150A TYR* 5.0 3.8 - - + -
153A ARG* 4.1 29.2 - - + -
155A PHE* 4.0 36.8 - - + -
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 2.9 23.2 + - - +
115A LEU* 3.8 9.2 - - + +
117A LEU* 1.3 80.0 - - - +
119A SER* 1.3 58.3 + - - +
121A LYS* 3.1 39.3 + - - +
122A ASP* 2.9 40.4 + - - +
153A ARG* 6.1 0.7 - - - +
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.6 22.1 - - - +
53A PHE* 4.2 5.5 - - - -
55A LEU* 3.6 22.6 - - - +
115A LEU* 2.9 24.0 + - - +
116A LEU 3.5 5.6 - - - -
118A GLU* 1.3 78.2 - - - +
120A LEU* 1.3 57.6 + - - +
122A ASP* 3.2 10.7 + - - +
123A HIS* 2.9 27.4 + - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.9 26.8 - - + -
67A ILE* 4.0 15.9 - - + -
69A ALA* 3.8 24.0 - - + -
71A ILE* 5.6 2.0 - - + -
96A ALA* 5.1 3.4 - - + -
98A ILE* 3.9 31.4 - - + -
116A LEU 3.1 9.3 + - - +
117A LEU* 3.2 12.8 + - + +
119A SER* 1.3 80.2 - - - +
121A LYS* 1.3 61.6 + - - +
123A HIS* 3.2 6.3 + - + +
124A ILE* 2.9 41.4 + - + +
135A ILE* 4.4 13.2 - - + -
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 3.1 31.3 + - + +
118A GLU* 3.1 37.9 + - - +
120A LEU* 1.3 75.2 - - - +
122A ASP* 1.3 65.4 + - - +
124A ILE* 3.3 10.7 + - - +
125A SER* 3.1 24.6 + - - -
135A ILE* 4.2 15.9 - - + -
153A ARG* 5.1 6.1 + - - +
154A ASP* 6.0 0.2 + - - -
155A PHE* 5.7 0.2 - - - -
179A LEU* 4.0 27.4 - - + +
181A ILE* 5.6 4.9 - - + -
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU* 2.9 26.6 + - - +
119A SER* 3.6 10.1 - - - +
121A LYS* 1.3 79.1 - - - +
123A HIS* 1.3 62.4 + - - +
125A SER* 3.2 7.5 + - - -
126A THR* 3.1 30.2 + - + +
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Residues in contact with HIS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.4 55.6 - + + +
71A ILE* 4.0 21.6 - - + +
119A SER 2.9 14.1 + - - +
120A LEU* 3.5 11.4 - - + +
122A ASP* 1.3 76.0 - - - +
124A ILE* 1.3 59.1 + - - +
126A THR* 3.4 6.1 + - - -
127A THR* 2.8 58.5 + - + +
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.0 23.3 - - + -
96A ALA* 3.7 21.8 - - + -
120A LEU* 2.9 32.7 + - + +
121A LYS* 3.6 6.1 - - - +
122A ASP 3.2 0.2 - - - -
123A HIS* 1.3 77.9 - - - +
125A SER* 1.3 59.2 + - - +
128A ALA* 2.8 28.6 + - + -
129A GLN 3.3 6.6 + - - +
132A CYS* 3.7 30.1 - - + -
135A ILE* 3.6 32.5 - - + -
181A ILE* 4.2 11.7 - - + -
182A ASN* 5.5 0.2 - - - +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LYS 3.1 13.9 + - - -
122A ASP* 3.2 11.1 + - - -
124A ILE* 1.3 78.6 - - - +
126A THR* 1.3 62.3 + - - +
129A GLN* 3.0 35.3 + - - +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASP* 3.1 16.1 + - + +
123A HIS* 3.4 12.1 + - - -
125A SER* 1.3 81.0 - - - +
127A THR* 1.3 64.5 + - - +
129A GLN* 3.5 13.3 + - - +
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.1 20.6 - - + -
94A GLN* 5.3 0.5 - - - +
123A HIS* 2.8 43.9 + - + +
124A ILE 4.2 0.9 - - - -
126A THR* 1.3 81.4 + - - +
128A ALA* 1.3 58.3 + - + +
129A GLN* 3.5 9.8 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.7 10.1 - - + -
94A GLN* 3.7 23.1 - - - +
124A ILE* 2.8 17.1 + - + +
127A THR* 1.3 75.0 - - + +
129A GLN* 1.3 80.5 + - - +
131A HIS* 3.0 21.7 + - - +
132A CYS* 4.0 23.1 - - + +
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 3.3 8.3 + - - +
125A SER* 3.0 26.0 + - - +
126A THR 3.5 20.6 + - - +
127A THR 3.5 11.2 + - - +
128A ALA* 1.3 87.3 - - - +
130A ASP* 1.3 70.4 + - - +
131A HIS* 3.2 18.9 + - + +
132A CYS 4.4 2.3 + - - -
182A ASN* 3.4 13.1 + - - -
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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