Contacts of the helix formed by residues 125 - 141 (chain A) in PDB entry 3EBV
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 ASN 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A VAL 3.5 19.3 + - - +
92A ASN* 4.3 13.9 + - + +
123A GLY 4.3 0.2 - - - -
124A LEU* 1.3 75.8 - - - +
126A PRO* 1.4 63.3 - - - +
127A THR* 2.9 23.2 + - - -
128A TYR* 3.2 25.5 + - - -
129A MSE 2.8 30.5 + - - +
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Residues in contact with PRO 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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124A LEU 3.4 11.0 - - - +
125A ASN* 1.4 82.9 - - - +
127A THR* 1.3 67.5 + - - +
129A MSE 4.6 0.2 - - - +
130A THR* 2.7 30.4 + - - +
161A GLY* 3.9 18.4 - - - +
164A GLN* 4.0 24.7 - - + -
165A THR* 3.3 24.7 - - - +
168A ASN* 4.3 3.5 + - - +
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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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125A ASN* 2.9 10.8 + - - -
126A PRO* 1.3 84.3 - - - +
128A TYR* 1.3 93.7 + - + +
130A THR* 4.1 2.6 - - - -
131A GLN* 3.5 18.1 + - - +
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Residues in contact with TYR 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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91A VAL* 3.6 16.4 - - + +
92A ASN 3.5 19.3 - - - -
93A SER* 3.3 36.1 - - - +
94A SER* 3.7 15.7 - - - -
97A ALA* 3.5 4.3 - - - +
125A ASN* 3.2 21.1 + - - -
127A THR* 1.3 99.3 - - + +
129A MSE 1.3 63.1 + - - +
130A THR 3.3 1.3 - - - -
131A GLN* 3.3 18.7 + - - -
132A ALA* 2.8 29.3 + - - +
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Residues in contact with MSE 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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91A VAL* 3.9 24.9 + - + +
100A PHE* 4.0 24.7 - - + -
118A ILE* 4.2 11.2 - - + -
120A LEU* 3.6 31.4 - - + -
124A LEU* 4.0 26.2 - - + -
125A ASN 2.8 19.5 + - - +
128A TYR* 1.3 78.8 - - - +
130A THR* 1.4 55.0 + - - +
132A ALA* 4.2 5.4 - - - -
133A LEU* 2.9 47.9 + - + +
148A MSE 4.9 3.6 - - + -
165A THR* 3.8 17.9 - - + +
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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
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126A PRO 2.7 24.7 + - - -
127A THR* 4.1 2.7 - - - -
129A MSE 1.4 77.7 - - - +
131A GLN* 1.3 65.1 + - - +
133A LEU* 3.3 1.6 + - - +
134A ARG* 3.0 32.8 + - + +
165A THR* 3.9 11.2 - - - +
168A ASN* 3.0 43.0 + - + +
169A VAL* 4.1 15.0 - - + -
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Residues in contact with GLN 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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94A SER* 3.0 35.5 + - - +
97A ALA* 4.1 9.7 - - + +
98A THR* 4.5 5.9 + - - -
127A THR* 3.5 11.1 + - - +
128A TYR* 3.3 29.0 + - - +
129A MSE 3.3 0.4 - - - -
130A THR* 1.3 81.4 - - - +
132A ALA* 1.3 62.6 + - - +
134A ARG* 3.3 6.6 + - - +
135A ALA* 3.0 24.1 + - + +
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Residues in contact with ALA 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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91A VAL* 3.9 11.0 - - + -
97A ALA* 3.5 34.5 - - + +
100A PHE* 3.9 17.0 - - + -
101A ALA* 3.6 3.8 - - - +
128A TYR 2.8 16.8 + - - +
129A MSE 3.7 6.5 - - - +
131A GLN* 1.3 76.7 - - - +
133A LEU* 1.3 59.3 + - - +
135A ALA* 3.3 4.6 + - - +
136A LEU* 2.9 29.2 + - - +
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Residues in contact with LEU 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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100A PHE* 4.4 8.7 - - + -
118A ILE* 4.0 17.5 - - + -
129A MSE 2.9 33.3 + - + +
130A THR 3.3 3.1 + - - +
132A ALA* 1.3 76.5 - - - +
134A ARG* 1.3 57.6 + - - +
136A LEU* 3.7 13.9 - - + +
137A SER* 2.8 30.3 + - - -
144A MSE 4.9 2.3 - - + +
146A LEU* 3.9 31.0 - - + -
148A MSE 4.7 7.9 - - + -
165A THR* 4.0 22.9 - - + -
169A VAL* 4.2 24.5 - - + -
172A ILE* 4.0 9.1 - - + +
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Residues in contact with ARG 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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130A THR* 3.0 29.6 + - + +
131A GLN* 3.3 6.3 + - - +
133A LEU* 1.3 72.8 - - - +
135A ALA* 1.3 61.0 + - - +
137A SER* 3.4 5.8 + - - -
138A ALA* 3.0 28.6 + - - +
168A ASN 2.9 23.2 + - - -
169A VAL* 3.6 13.8 - - + +
171A ASP* 2.7 43.0 + - - -
172A ILE* 3.8 25.1 - - - +
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Residues in contact with ALA 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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97A ALA 5.0 2.0 - - - +
98A THR* 5.5 6.3 - - - +
101A ALA* 3.6 15.9 - - + -
131A GLN* 3.0 16.0 + - + +
132A ALA* 3.3 9.6 + - - +
134A ARG* 1.3 77.6 - - - +
136A LEU* 1.3 61.8 + - - +
138A ALA* 3.3 8.8 + - - +
139A LYS* 3.3 28.8 + - - +
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Residues in contact with LEU 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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100A PHE* 4.6 6.7 - - + -
101A ALA* 3.5 28.6 - - + +
104A VAL* 3.6 25.1 - - + -
105A TYR* 3.7 26.9 - - + +
108A MSE 4.2 8.5 - - - -
116A VAL* 3.7 23.3 - - + -
132A ALA 2.9 17.4 + - - +
133A LEU* 3.7 13.9 - - + +
135A ALA* 1.3 77.0 - - - +
137A SER* 1.3 62.0 - - - +
139A LYS* 3.0 7.3 + - - +
140A ALA* 3.0 19.8 + - - +
144A MSE 3.7 16.6 - - + -
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Residues in contact with SER 137 (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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133A LEU 2.8 20.9 + - - -
134A ARG* 3.7 8.4 + - - -
136A LEU* 1.3 73.3 - - - +
138A ALA* 1.3 57.0 + - - +
140A ALA 4.5 0.4 - - - +
141A GLY* 2.8 40.3 + - - +
142A PRO* 5.6 0.3 - - - +
144A MSE 4.3 14.9 - - - +
172A ILE* 3.7 36.2 - - - +
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Residues in contact with ALA 138 (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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134A ARG 3.0 14.4 + - - +
135A ALA* 3.5 12.6 - - - +
136A LEU 3.2 0.2 - - - -
137A SER* 1.3 77.1 - - - +
139A LYS* 1.3 61.9 + - + +
141A GLY* 4.4 2.6 + - - -
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Residues in contact with LYS 139 (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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101A ALA* 4.0 18.8 - - - +
102A ASN* 2.9 29.1 + - - -
105A TYR* 3.4 58.9 + - + -
135A ALA* 3.3 18.6 + - - +
136A LEU* 3.0 7.0 + - - +
138A ALA* 1.3 79.7 - - + +
140A ALA* 1.3 59.8 + - - +
141A GLY 3.5 0.2 - - - -
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Residues in contact with ALA 140 (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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105A TYR* 3.7 14.1 - - + -
108A MSE 3.9 19.3 - - + -
136A LEU* 3.0 9.1 + - + +
137A SER 4.6 0.2 - - - +
139A LYS* 1.3 76.4 - - - +
141A GLY* 1.3 62.7 + - - +
143A ASP* 4.9 2.6 + - - +
144A MSE 3.7 38.8 + - + +
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Residues in contact with GLY 141 (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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137A SER* 2.8 24.8 + - - +
138A ALA 4.4 2.6 + - - -
139A LYS 3.5 2.0 - - - -
140A ALA* 1.3 77.8 - - - +
142A PRO* 1.3 74.4 - - - +
143A ASP 3.2 5.4 + - - -
144A MSE 3.2 17.2 + - - +
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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