Contacts of the helix formed by residues 127 - 145 (chain A) in PDB entry 3VOC
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 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 4.7 4.9 + - - -
125A LEU 3.4 5.4 + - - -
126A TRP* 1.3 85.0 + - - +
128A GLY* 1.3 61.1 + - - +
129A THR 3.7 0.3 + - - -
130A GLY 4.5 4.3 + - - -
131A LYS* 4.7 5.7 + - - +
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Residues in contact with GLY 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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126A TRP* 3.0 29.2 - - - -
127A SER* 1.3 82.7 + - - +
129A THR* 1.3 58.3 + - - +
130A GLY 3.5 0.4 - - - -
131A LYS* 3.4 11.1 + - - +
132A GLN* 2.9 34.9 + - - +
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Residues in contact with THR 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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122A LEU* 3.4 22.2 - - + +
123A SER 2.7 25.6 + - - +
124A PRO* 4.8 3.6 - - - -
126A TRP* 3.2 21.9 + - - +
128A GLY* 1.3 75.7 - - - +
130A GLY* 1.3 64.0 + - - +
132A GLN* 3.2 1.7 + - - +
133A TYR* 3.0 52.5 + - + +
256A HIS* 3.8 26.9 - - + +
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TRP 4.7 1.2 + - - -
127A SER 4.5 3.0 + - - -
128A GLY 3.5 0.4 - - - -
129A THR* 1.3 78.9 - - - +
131A LYS* 1.3 56.0 + - - +
133A TYR* 3.3 5.9 + - - +
134A ASP* 2.9 30.9 + - - +
259A VAL* 3.8 29.1 - - - +
260A ILE* 5.7 1.6 - - - -
263A ALA* 4.9 4.0 - - - +
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Residues in contact with LYS 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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127A SER 4.7 4.9 + - - +
128A GLY* 3.4 16.2 + - - +
129A THR 3.2 0.4 - - - -
130A GLY* 1.3 76.0 - - - +
132A GLN* 1.3 67.9 + - + +
134A ASP* 3.2 8.5 + - + +
135A GLU* 3.0 49.1 + - + +
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Residues in contact with GLN 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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44A TRP* 3.8 22.4 - - + -
48A GLU* 3.8 1.0 - - - +
52A ASP* 3.2 26.2 + - - +
98A TRP* 3.4 19.7 - - - -
99A LEU* 4.1 15.6 - - + +
102A LYS* 5.4 3.4 - - - +
126A TRP* 4.1 11.7 - - + -
128A GLY* 2.9 21.4 + - - +
129A THR* 3.7 4.9 - - - +
131A LYS* 1.3 82.6 - - - +
133A TYR* 1.3 62.1 + - - +
135A GLU* 3.4 12.9 + - - +
136A LEU* 3.0 22.7 + - - +
501A CA 2.3 25.3 - - - -
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Residues in contact with TYR 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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44A TRP* 3.9 17.9 - + - -
80A THR* 3.3 51.0 + - + -
121A ALA* 4.7 3.1 - - - +
122A LEU* 4.2 16.0 + - + +
129A THR* 3.0 41.3 + - + +
130A GLY* 3.9 4.3 - - - +
132A GLN* 1.3 75.1 - - - +
134A ASP* 1.3 61.1 + - - +
136A LEU* 3.2 5.7 + - - -
137A TYR* 2.8 60.0 + + + -
157A SER 4.0 10.9 + - - -
158A GLY 5.8 0.2 - - - -
159A GLY 5.7 1.2 + - - -
256A HIS* 4.0 12.2 + + - -
260A ILE* 3.4 32.8 - - + -
263A ALA* 5.4 1.6 - - + -
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Residues in contact with ASP 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 GLY 2.9 18.4 + - - +
131A LYS* 3.4 8.6 - - - +
133A TYR* 1.3 76.2 - - - +
135A GLU* 1.3 59.3 + - + +
138A ALA* 3.0 29.0 + - - +
263A ALA* 4.1 18.2 - - + +
266A LYS* 2.8 31.9 + - - -
267A ASN* 2.8 32.4 + - - +
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Residues in contact with GLU 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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52A ASP* 3.5 3.5 - - - +
53A ASN* 3.1 33.5 + - - +
55A PHE* 4.0 4.1 - - + -
131A LYS* 3.0 42.8 + - + +
132A GLN* 3.1 19.8 + - - +
134A ASP* 1.3 74.9 - - + +
136A LEU* 1.3 58.4 + - - +
138A ALA* 3.5 7.1 + - - +
139A SER* 2.9 28.6 + - - -
501A CA 2.2 29.2 - - - -
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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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42A VAL 6.0 0.2 - - - +
44A TRP* 3.7 24.9 - - + +
47A VAL* 3.8 16.2 - - + -
48A GLU* 4.3 5.6 + - - +
55A PHE* 3.9 19.5 - - + -
57A TRP* 3.7 23.1 - - + -
78A ILE* 3.5 28.7 - - + -
80A THR* 3.5 24.7 - - + -
132A GLN 3.0 16.6 + - - +
133A TYR* 3.7 5.6 - - - +
135A GLU* 1.3 74.4 - - - +
137A TYR* 1.3 61.6 + - + +
139A SER* 3.3 1.4 + - - -
140A PHE* 2.9 27.9 + - - +
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Residues in contact with TYR 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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78A ILE* 3.6 36.3 + - + -
80A THR* 5.1 2.2 + - + -
133A TYR* 2.8 52.6 + + + +
136A LEU* 1.3 75.9 - - + +
138A ALA* 1.3 60.9 + - - +
140A PHE* 3.3 2.1 + - - +
141A ALA* 2.9 26.3 + - - +
156A LEU* 3.6 22.0 - - + +
157A SER 4.9 2.1 + - - -
260A ILE* 3.5 30.7 - - - +
263A ALA* 3.8 11.9 - - + -
264A ALA* 3.6 24.9 - - + -
267A ASN* 3.8 15.3 - - + +
268A PHE* 3.3 30.1 - + + -
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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 ASP* 3.0 17.3 + - - +
135A GLU* 3.5 8.7 - - - +
137A TYR* 1.3 77.6 - - - +
139A SER* 1.3 62.3 + - - +
141A ALA* 3.3 4.1 + - - +
142A GLU* 3.0 25.7 + - - +
267A ASN* 3.3 24.5 - - - +
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Residues in contact with SER 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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55A PHE* 3.3 35.8 - - - -
57A TRP* 2.9 21.2 + - - -
135A GLU 2.9 18.2 + - - -
136A LEU 3.7 3.6 - - - -
138A ALA* 1.3 78.3 - - - +
140A PHE* 1.3 57.2 - - - +
142A GLU* 3.3 7.5 + - - -
143A ASN* 2.9 41.9 + - - +
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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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42A VAL* 4.9 2.2 - - + -
57A TRP* 3.7 28.6 - + + -
74A TRP* 4.0 17.5 - + - -
76A PRO* 3.6 30.3 - - + -
78A ILE* 3.9 24.5 - - + -
136A LEU 2.9 16.9 + - - +
137A TYR* 3.3 7.4 + - - +
139A SER* 1.3 75.1 - - - +
141A ALA* 1.3 59.8 + - - +
143A ASN 3.2 0.9 + - - -
144A PHE* 2.8 67.9 + + + +
151A ILE* 4.2 4.7 - - + -
154A ILE* 4.6 6.5 - - + -
268A PHE* 4.0 15.5 - + + -
272A PHE* 4.1 21.5 - + - -
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Residues in contact with ALA 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 TYR 2.9 18.4 + - - +
138A ALA* 3.6 6.3 - - - +
140A PHE* 1.3 75.9 - - - +
142A GLU* 1.3 58.6 + - - +
145A ALA* 3.0 34.5 + - - +
267A ASN* 3.4 25.6 - - + +
268A PHE* 4.0 7.2 - - + -
271A VAL* 3.9 12.1 - - + +
272A PHE* 3.8 15.9 - - + -
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Residues in contact with GLU 142 (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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138A ALA 3.0 17.1 + - - +
139A SER* 3.6 8.5 + - - +
141A ALA* 1.3 79.4 - - - +
143A ASN* 1.3 67.4 + - - +
144A PHE 3.6 0.2 + - - -
145A ALA* 4.1 9.7 + - - +
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Residues in contact with ASN 143 (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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55A PHE* 5.5 0.4 - - - +
57A TRP* 3.3 30.9 - - + +
61A LYS* 2.9 43.3 + - - +
139A SER* 2.9 33.9 + - - +
142A GLU* 1.3 87.5 + - - +
144A PHE* 1.3 73.4 + - + +
145A ALA 3.6 0.2 - - - -
146A GLY 4.9 1.6 + - - -
147A TYR* 4.4 6.6 - - - -
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Residues in contact with PHE 144 (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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57A TRP* 3.5 35.7 - + + -
60A TYR* 3.9 24.7 - - + -
61A LYS* 3.8 32.5 - - + -
64A ALA* 4.3 3.4 - - + -
74A TRP* 3.8 26.9 - + - -
140A PHE* 2.8 45.7 + + + +
143A ASN* 1.3 83.3 - - + +
145A ALA* 1.3 56.2 + - - +
146A GLY 3.2 2.9 - - - -
147A TYR* 2.8 47.4 + + + +
151A ILE* 4.6 2.2 - - + -
272A PHE* 3.4 18.2 - - + -
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Residues in contact with ALA 145 (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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141A ALA 3.0 18.1 + - - +
142A GLU* 4.2 8.3 - - - +
143A ASN 3.6 0.8 - - - -
144A PHE* 1.3 76.4 - - - +
146A GLY* 1.3 56.9 + - - +
147A TYR 3.1 4.5 + - - -
148A LYS* 3.2 21.1 + - - +
271A VAL* 3.7 23.0 - - + +
272A PHE* 4.1 1.6 - - - -
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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