Contacts of the helix formed by residues 124 - 140 (chain A) in PDB entry 2VPA
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 ALA 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A VAL 5.5 0.4 - - - +
123A LEU* 1.3 76.2 - - - +
125A GLY* 1.3 68.6 + - - +
126A GLU 3.4 0.5 + - - -
127A ASP* 3.1 22.4 + - - +
128A ALA* 3.3 5.0 + - - -
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Residues in contact with GLY 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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124A ALA* 1.3 73.9 - - - +
126A GLU* 1.3 60.0 + - - -
128A ALA* 3.0 6.7 + - - +
129A ARG* 2.9 25.9 + - - +
154A GLU* 5.4 4.9 - - - -
157A LEU* 3.5 22.9 - - - +
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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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124A ALA 3.4 0.6 + - - -
125A GLY* 1.3 71.6 - - - -
127A ASP* 1.3 58.5 + - - +
129A ARG* 2.9 40.4 + - - +
130A ALA* 2.9 31.5 + - - +
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Residues in contact with ASP 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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62A ARG* 5.1 1.9 + - - -
121A ARG* 5.5 2.3 + - - -
123A LEU* 3.8 25.3 - - + +
124A ALA 3.1 13.7 + - - +
126A GLU* 1.3 79.3 - - - +
128A ALA* 1.3 57.6 + - - +
130A ALA* 3.5 4.2 + - - +
131A ALA* 3.1 28.8 + - - +
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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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123A LEU* 3.8 34.5 - - + +
124A ALA* 3.3 7.3 + - - -
125A GLY 3.0 9.1 + - - +
127A ASP* 1.3 77.9 - - - +
129A ARG* 1.4 60.0 + - - +
131A ALA* 3.8 1.0 - - - +
132A LEU* 2.9 33.8 + - - +
157A LEU* 4.0 17.0 - - + -
162A VAL* 4.1 13.9 - - + +
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Residues in contact with ARG 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 GLY* 2.9 10.1 + - - +
126A GLU* 2.9 42.8 + - - +
128A ALA* 1.4 76.2 - - - +
130A ALA* 1.3 57.6 + - - +
132A LEU* 3.4 4.1 + - - +
133A THR* 2.8 39.5 + - - +
145A VAL* 6.3 0.4 - - + -
151A PRO* 6.1 0.4 - - - +
152A ILE* 2.9 44.7 + - + +
153A SER* 3.8 7.9 - - - +
154A GLU* 3.0 28.3 + - - +
157A LEU* 3.7 26.6 - - + +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.7 6.5 - - - +
126A GLU 2.9 18.3 + - - +
127A ASP* 4.0 4.0 - - - +
129A ARG* 1.3 77.3 - - - +
131A ALA* 1.3 57.4 + - - +
133A THR* 3.3 5.9 + - - -
134A THR* 2.9 35.2 + - - +
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Residues in contact with ALA 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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62A ARG* 4.0 12.9 - - - +
69A VAL* 3.8 26.6 - - + +
123A LEU* 3.5 22.7 - - + -
127A ASP 3.1 18.2 + - - +
128A ALA 3.8 3.1 - - - +
129A ARG 3.3 0.2 - - - -
130A ALA* 1.3 76.3 - - - +
132A LEU* 1.3 56.5 + - - +
134A THR* 3.3 4.3 + - - +
135A LEU* 2.9 29.3 + - - +
162A VAL* 4.1 6.3 - - + -
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Residues in contact with LEU 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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71A HIS* 3.7 35.0 - - + +
128A ALA 2.9 19.2 + - - +
129A ARG 3.8 3.4 - - - +
131A ALA* 1.3 74.4 - - - +
133A THR* 1.3 57.4 + - - +
135A LEU* 3.5 9.5 + - + +
136A SER* 2.8 38.5 + - - +
152A ILE* 3.9 20.9 - - + -
156A ASP* 5.8 1.8 - - + +
157A LEU* 4.0 19.3 - - + -
160A THR* 4.6 10.3 - - + +
162A VAL* 3.6 32.1 - - + -
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Residues in contact with THR 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 ARG* 2.8 27.3 + - - +
130A ALA* 3.6 7.0 - - - -
132A LEU* 1.3 73.7 - - - +
134A THR* 1.3 66.3 + - - +
136A SER* 3.3 0.9 + - - -
137A GLU* 2.9 55.8 + - - +
145A VAL* 4.0 21.9 - - + +
152A ILE* 3.5 13.5 - - - +
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Residues in contact with THR 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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60A ALA* 4.5 5.8 - - + -
62A ARG* 4.1 26.9 + - + -
69A VAL* 5.1 0.4 - - + -
130A ALA* 2.9 18.5 + - - +
131A ALA* 3.7 5.8 - - - -
133A THR* 1.3 76.6 - - - +
135A LEU* 1.3 64.4 + - - +
137A GLU* 3.9 3.8 - - - +
138A ARG* 3.0 48.2 + - - +
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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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58A ALA* 3.8 9.4 - - + +
59A TYR* 3.2 47.6 - - - +
60A ALA* 3.6 9.6 - - - +
69A VAL* 4.0 7.2 - - + +
70A TYR* 4.3 15.7 - - - +
71A HIS* 3.7 30.5 - - + +
131A ALA 2.9 17.2 + - - +
132A LEU* 3.6 11.9 - - + +
134A THR* 1.3 76.3 - - - +
136A SER* 1.3 64.9 - - - +
138A ARG* 3.2 3.8 + - - +
139A VAL* 3.1 29.4 + - + +
1197A PYR 3.9 12.8 - - - +
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Residues in contact with SER 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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132A LEU* 2.8 25.8 + - - +
133A THR 3.8 2.9 - - - -
135A LEU* 1.3 77.6 - - - +
137A GLU* 1.3 57.7 + - - +
139A VAL* 4.4 6.1 - - - -
140A PHE* 3.0 39.1 + - - +
143A LEU* 4.4 8.5 - - - +
145A VAL* 4.2 17.9 - - - +
152A ILE* 5.5 1.9 - - - +
1197A PYR 4.4 10.7 + - - -
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Residues in contact with GLU 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 THR* 2.9 39.7 + - + +
134A THR* 4.2 3.6 - - - +
136A SER* 1.3 77.0 - - - +
138A ARG* 1.3 59.7 + - - +
140A PHE 3.5 14.6 - - - +
141A PRO* 3.8 7.3 - - - +
142A GLY 4.6 1.7 + - - -
143A LEU* 3.3 25.3 - - + +
144A LYS* 3.4 24.0 + - + +
145A VAL* 2.8 33.3 + - + +
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Residues in contact with ARG 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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31A LEU 5.4 0.4 + - - -
32A LEU* 4.2 28.9 + - - +
34A GLY 5.4 5.8 - - - +
35A THR* 4.8 6.9 - - + +
59A TYR 4.7 1.1 - - - +
60A ALA* 3.9 19.2 - - + +
61A TYR* 2.8 42.0 + - - +
62A ARG* 5.0 3.2 - - - +
63A PRO* 5.1 2.4 - - - +
134A THR* 3.0 36.3 + - - +
135A LEU 3.4 4.5 - - - +
137A GLU* 1.3 77.3 - - - +
139A VAL* 1.3 66.8 + - + +
141A PRO* 3.9 13.5 - - - +
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Residues in contact with VAL 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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35A THR* 3.9 34.6 - - + +
58A ALA* 4.6 4.7 - - + -
59A TYR 3.8 22.4 - - - +
135A LEU* 3.1 24.4 + - + +
136A SER 4.0 0.4 - - - +
138A ARG* 1.3 79.1 - - + +
140A PHE* 1.3 86.2 + - + +
141A PRO* 3.4 10.5 - - - +
1197A PYR 3.9 21.8 - - + +
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Residues in contact with PHE 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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136A SER* 3.0 22.1 + - - +
137A GLU 3.5 8.9 - - - +
139A VAL* 1.3 91.6 - - + +
141A PRO* 1.4 69.4 - - - +
143A LEU* 2.9 44.0 + - + +
1197A PYR 3.7 31.4 - - + -
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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