Contacts of the helix formed by residues 119 - 136 (chain A) in PDB entry 4R8U
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 SER 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A HIS 3.8 0.6 + - - -
116A CYS 2.7 16.7 + - - +
117A HIS* 3.1 4.1 + - - -
118A GLY* 1.3 76.6 - - - +
120A ALA* 1.3 56.9 + - - +
121A THR* 3.3 8.0 + - - -
122A LEU* 2.8 38.6 + - - +
123A ILE* 2.9 29.9 + - - +
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Residues in contact with ALA 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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4A LYS* 3.9 18.8 - - + +
6A ILE* 3.7 4.8 - - + +
110A VAL* 3.8 26.2 - - + -
118A GLY 3.2 5.5 + - - -
119A SER* 1.3 69.5 - - - +
121A THR* 1.3 64.8 + - - +
123A ILE* 4.3 6.1 - - - -
124A ALA* 3.2 24.6 + - - +
143A VAL* 3.7 26.4 - - + +
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 3.2 7.5 + - - -
120A ALA* 1.3 80.8 - - - +
122A LEU* 1.3 71.4 + - + +
124A ALA 3.4 0.3 + - - -
125A GLN* 3.2 12.6 + - - +
143A VAL* 4.5 6.1 - - - +
162A GLN* 3.1 36.9 + - - +
164A VAL* 3.3 31.2 - - + +
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Residues in contact with LEU 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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116A CYS* 3.8 25.8 - - + +
117A HIS* 6.2 0.9 - - + +
119A SER* 2.8 28.7 + - - +
121A THR* 1.3 78.5 - - + +
123A ILE* 1.3 65.8 + - - +
125A GLN* 3.3 13.3 + - + +
126A GLU* 3.0 24.8 + - - +
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Residues in contact with ILE 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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6A ILE* 3.7 17.0 - - + -
94A TYR* 4.1 14.9 - - + -
110A VAL* 4.2 29.2 - - + +
113A SER* 4.3 11.2 - - - +
115A HIS* 3.8 26.2 - - + +
116A CYS* 3.8 20.4 - - - -
118A GLY 4.8 2.7 - - - -
119A SER 2.9 30.4 + - - +
120A ALA* 3.9 4.9 - - - +
121A THR 3.3 0.2 - - - -
122A LEU* 1.3 76.4 - - - +
124A ALA* 1.3 62.7 + - - +
126A GLU* 3.2 5.0 + - - +
127A ILE* 3.0 36.4 + - + +
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Residues in contact with ALA 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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6A ILE* 4.1 20.4 - - + -
8A VAL* 6.0 0.8 - - - +
120A ALA 3.2 16.3 + - - +
121A THR 3.6 5.2 - - - +
123A ILE* 1.3 80.2 - - - +
125A GLN* 1.3 57.7 + - - +
127A ILE* 3.4 6.7 + - - +
128A ARG* 3.1 33.4 + - - +
141A ALA* 4.2 7.7 - - + +
143A VAL* 4.0 17.5 - - + -
162A GLN* 3.6 12.8 - - - +
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Residues in contact with GLN 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 THR* 3.2 11.3 + - + +
122A LEU* 3.5 19.6 - - + +
123A ILE 3.2 0.6 - - - -
124A ALA* 1.3 78.0 - - - +
126A GLU* 1.3 60.0 + - - +
128A ARG* 3.0 30.9 + - - +
129A GLN* 3.0 28.0 + - + +
162A GLN* 3.3 23.3 + - - +
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Residues in contact with GLU 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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94A TYR* 2.6 38.6 + - + +
115A HIS* 5.7 1.2 - - - -
116A CYS* 3.4 20.4 - - - -
122A LEU 3.0 14.9 + - - +
123A ILE* 3.2 4.7 + - - +
125A GLN* 1.3 74.5 - - - +
127A ILE* 1.3 58.4 + - - +
129A GLN* 3.8 7.2 - - + +
130A THR* 2.6 42.3 + - - +
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Residues in contact with ILE 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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6A ILE* 5.1 1.1 - - + -
8A VAL* 4.5 12.6 - - + -
90A ILE* 4.7 5.3 - - + +
91A PHE* 3.8 29.6 - - + -
94A TYR* 3.7 30.1 - - + -
108A LEU* 3.6 31.4 - - + -
123A ILE* 3.0 33.6 + - + +
124A ALA* 3.7 8.3 - - - +
126A GLU* 1.3 78.1 - - - +
128A ARG* 1.3 58.1 + - + +
130A THR* 3.3 5.6 + - - -
131A ILE* 2.9 39.8 + - + +
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Residues in contact with ARG 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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8A VAL* 5.2 2.0 - - + -
124A ALA 3.1 11.9 + - - +
125A GLN* 3.0 35.8 - - - +
127A ILE* 1.3 78.2 - - + +
129A GLN* 1.3 56.5 + - - +
131A ILE* 3.8 7.9 - - - +
132A PHE* 3.0 27.2 + - - +
137A LEU 5.0 0.5 - - - +
138A THR* 5.6 0.3 - - - -
139A ALA* 2.9 37.5 + - + +
141A ALA* 4.0 22.9 - - + +
160A ASN* 2.9 45.2 + - - +
161A GLY* 3.3 11.7 + - - +
162A GLN* 3.0 31.8 + - - +
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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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125A GLN* 3.0 19.4 + - + +
126A GLU* 3.8 8.1 - - + +
128A ARG* 1.3 73.9 - - - +
130A THR* 1.3 57.1 + - - +
132A PHE* 3.1 17.4 + - - +
133A ASN* 2.7 74.8 + - - +
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Residues in contact with THR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 4.0 17.7 - - + -
93A ARG* 3.6 15.5 - - - +
94A TYR* 4.0 11.5 + - + +
126A GLU* 2.6 25.9 + - - +
127A ILE* 3.7 4.3 - - - -
129A GLN* 1.3 78.0 - - - +
131A ILE* 1.3 52.3 + - - +
133A ASN* 3.2 9.7 + - + +
134A GLU* 2.7 59.7 + - + +
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Residues in contact with ILE 131 (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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8A VAL* 4.5 1.3 - - + -
10A MET* 3.8 23.6 - - + -
87A ILE* 4.1 17.9 - - + -
90A ILE* 4.0 20.9 - - + -
91A PHE* 4.1 13.9 - - + -
127A ILE* 2.9 36.9 + - + +
128A ARG* 3.8 5.2 - - - +
130A THR* 1.3 72.5 - - - +
132A PHE* 1.3 66.9 + - - +
135A LEU* 2.9 40.2 + - + +
136A GLN 3.6 0.5 + - - -
137A LEU 3.7 13.2 - - - +
138A THR 5.1 0.2 - - - -
139A ALA* 4.3 20.4 - - + -
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Residues in contact with PHE 132 (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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26A ARG* 6.1 2.5 - - - -
128A ARG 3.0 14.9 + - - +
129A GLN* 3.5 26.5 - - - +
131A ILE* 1.3 76.6 - - - +
133A ASN* 1.3 63.8 + - - +
136A GLN* 2.8 50.7 + - + +
137A LEU 3.3 17.5 - - - +
138A THR* 4.0 21.5 - - + -
160A ASN* 6.0 3.6 - - - +
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Residues in contact with ASN 133 (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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129A GLN* 2.7 53.9 + - - +
130A THR* 3.5 8.4 - - - +
132A PHE* 1.3 79.3 - - - +
134A GLU* 1.3 65.4 + - + +
136A GLN* 3.4 12.5 + - - +
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Residues in contact with GLU 134 (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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86A HIS* 2.8 40.9 + - + +
90A ILE* 3.8 1.8 - - + +
93A ARG* 2.7 40.3 + - - -
130A THR* 2.7 32.1 + - + +
133A ASN* 1.3 80.1 - - + +
135A LEU* 1.3 62.5 + - + +
136A GLN* 3.8 6.8 + - - -
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Residues in contact with LEU 135 (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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20A ARG* 3.1 27.5 + - - +
83A ALA* 3.5 42.6 - - + +
86A HIS* 3.9 21.1 - - + +
87A ILE* 4.0 11.4 - - + -
90A ILE* 3.7 28.9 - - + -
131A ILE* 2.9 24.0 + - + +
134A GLU* 1.3 82.3 - - - +
136A GLN* 1.3 72.3 + - - +
137A LEU* 3.2 17.4 + - + +
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Residues in contact with GLN 136 (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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20A ARG* 4.1 23.0 + - + +
26A ARG* 4.5 13.0 + - - +
132A PHE* 2.8 34.8 + - + +
133A ASN 3.4 18.6 + - - +
134A GLU 3.8 7.9 + - - -
135A LEU* 1.3 81.8 - - - +
137A LEU* 1.3 66.0 + - - +
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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