Contacts of the helix formed by residues 116 - 131 (chain A) in PDB entry 3CWR
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 ASP 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A MSE 3.3 12.3 + - - +
113A LEU 3.5 8.2 + - - +
114A ALA 3.5 0.8 + - - -
115A SER* 1.3 82.2 - - - +
117A ALA* 1.3 57.2 + - - +
118A ASP* 2.9 22.9 + - - +
119A LEU* 3.1 33.9 + - + +
120A ARG* 3.0 26.4 + - - -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ASP* 1.3 72.3 + - - +
118A ASP* 1.3 56.5 + - - +
120A ARG* 3.4 30.8 + - - +
121A ASN* 2.9 28.8 + - - +
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Residues in contact with ASP 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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60A ARG* 5.4 2.3 + - - -
116A ASP* 2.9 11.8 + - - +
117A ALA* 1.3 75.7 - - - +
119A LEU* 1.3 72.4 + - - +
121A ASN* 3.3 14.0 + - - +
122A ARG* 3.0 37.6 + - - +
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Residues in contact with LEU 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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34A ALA* 3.8 28.7 - - + -
60A ARG* 4.6 9.4 - - - +
112A MSE 3.6 30.3 - - + +
113A LEU* 3.9 14.1 - - + -
116A ASP* 3.1 35.0 + - + +
118A ASP* 1.3 88.0 - - - +
120A ARG* 1.3 61.4 + - - +
122A ARG* 4.5 3.1 - - + -
123A PHE* 2.8 50.8 + - + +
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Residues in contact with ARG 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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113A LEU* 2.8 58.2 + - + +
114A ALA* 3.1 22.6 + - - +
115A SER 4.4 0.6 - - - -
116A ASP 3.0 7.3 + - - +
117A ALA* 3.6 40.1 + - - +
119A LEU* 1.3 75.0 - - - +
121A ASN* 1.3 66.6 + - - +
124A LEU* 2.9 50.9 + - + +
125A PRO* 4.1 0.7 - - - +
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Residues in contact with ASN 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 ALA 2.9 17.1 + - - +
118A ASP* 3.5 14.9 + - - +
119A LEU 3.3 0.2 - - - -
120A ARG* 1.3 78.8 - - - +
122A ARG* 1.3 66.6 + - - +
125A PRO* 4.3 9.5 - - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLY* 5.2 3.4 - - - -
60A ARG* 2.8 71.3 - - - +
61A ALA* 3.5 22.8 - - - +
118A ASP* 3.0 27.8 + - - +
119A LEU* 3.8 5.6 - - + +
121A ASN* 1.3 85.0 - - - +
123A PHE* 1.3 76.0 + - + +
125A PRO* 4.5 5.6 - - - +
210A SO4 4.6 13.1 + - - -
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Residues in contact with PHE 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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29A LEU* 6.0 0.4 - - + -
34A ALA* 4.3 10.3 - - + -
37A MSE 4.3 7.2 - - + -
60A ARG* 3.6 50.0 - - + -
61A ALA* 3.8 18.8 - - - -
64A ILE* 3.8 29.1 - - + +
109A LEU* 5.5 2.0 - - + -
112A MSE 5.5 2.9 - - - -
113A LEU* 4.0 20.0 - - + -
119A LEU* 2.8 42.9 + - + +
122A ARG* 1.3 96.1 - - + +
124A LEU* 1.3 63.8 + - - +
125A PRO* 3.4 3.1 - - - -
126A ALA* 3.3 5.6 + - - +
127A TYR* 3.0 22.4 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU* 5.0 7.2 - - + +
119A LEU 4.1 0.2 + - - -
120A ARG* 2.9 40.7 + - + +
123A PHE* 1.3 76.1 - - - +
125A PRO* 1.3 62.3 - - + +
127A TYR* 3.2 22.8 + - + -
128A ASN* 2.8 45.2 + - + +
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Residues in contact with PRO 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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120A ARG 4.1 4.7 - - - +
121A ASN 4.3 10.3 - - - +
122A ARG 4.5 3.1 - - - +
123A PHE* 3.5 4.5 - - - -
124A LEU* 1.3 93.6 - - + +
126A ALA* 1.3 56.7 + - - +
128A ASN* 3.8 5.1 - - + +
129A ALA* 3.0 32.5 + - - +
125B PRO* 3.7 35.0 - - + -
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Residues in contact with ALA 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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61A ALA* 3.2 38.6 - - + +
62A ASP* 5.1 2.9 - - - +
64A ILE* 4.9 1.1 - - + -
65A GLY* 3.9 12.0 - - - +
122A ARG 5.7 0.2 + - - -
123A PHE 3.3 6.8 + - - +
124A LEU 3.3 0.4 - - - -
125A PRO* 1.3 81.0 - - - +
127A TYR* 1.3 61.9 + - - +
129A ALA* 4.7 1.3 - - - -
130A ASN* 2.9 36.0 + - - +
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Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ILE* 4.2 11.6 - - + +
68A VAL* 3.8 27.7 - - + +
71A TRP* 5.4 2.7 - + - -
106A ALA 4.7 3.0 + - - -
109A LEU* 3.8 29.2 - - + -
110A PHE* 3.6 35.3 - + - +
113A LEU* 3.6 29.2 - - + -
123A PHE 3.0 17.2 + - - +
124A LEU* 3.5 15.9 - - + +
126A ALA* 1.3 78.3 - - - +
128A ASN* 1.3 65.7 + - + +
131A GLY* 3.3 21.3 + - - -
174A LEU* 5.6 1.4 - - - +
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Residues in contact with ASN 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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124A LEU* 2.8 30.5 + - + +
125A PRO* 3.8 5.2 - - + +
127A TYR* 1.3 82.5 - - + +
129A ALA* 1.3 63.7 + - - +
130A ASN 3.3 0.3 + - - -
131A GLY* 3.7 4.0 + - - -
132A ILE* 4.8 7.8 + - - +
133A GLU* 3.2 49.2 + - - +
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Residues in contact with ALA 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 PRO 3.0 18.9 + - - +
126A ALA* 4.7 0.7 - - - -
128A ASN* 1.3 78.8 - - - +
130A ASN* 1.3 70.6 + - - +
131A GLY 3.5 0.4 + - - -
133A GLU* 3.7 17.0 - - - +
134A ARG* 3.2 25.6 + - - +
137A ARG* 4.7 2.4 + - - -
129B ALA* 3.9 28.5 - - + -
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Residues in contact with ASN 130 (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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65A GLY* 3.5 35.4 - - - +
68A VAL* 3.5 9.0 - - + +
69A GLU* 3.8 11.9 - - - +
72A ILE* 3.3 25.1 - - - +
126A ALA* 2.9 31.5 + - - +
128A ASN 3.2 0.2 - - - -
129A ALA* 1.3 88.3 - - - +
131A GLY* 1.3 58.7 + - - +
134A ARG* 3.2 26.5 + - - +
137B ARG* 5.3 0.5 + - - -
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Residues in contact with GLY 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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68A VAL* 3.3 17.5 - - - -
72A ILE* 4.3 9.0 - - - +
101A VAL* 6.0 0.7 - - - -
127A TYR 3.3 12.2 + - - -
128A ASN 3.7 1.0 + - - -
129A ALA 3.5 1.8 - - - -
130A ASN* 1.3 79.2 - - - +
132A ILE* 1.3 58.9 + - - -
133A GLU 3.1 2.7 - - - -
134A ARG* 2.8 28.6 + - - +
135A SER* 3.2 12.1 + - - -
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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