Contacts of the helix formed by residues 131 - 148 (chain D) in PDB entry 6VSU
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 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D GLY 3.7 3.4 + - - +
130D VAL* 1.3 80.1 - - - +
132D ASP* 1.3 59.7 + - - +
133D ASP* 3.4 15.4 + - - +
134D ARG* 3.0 29.4 + - - +
135D LEU* 3.0 24.0 + - - +
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D HIS* 2.8 37.3 + - - -
75D ASN* 4.2 14.2 + - - +
130D VAL 5.4 0.7 - - - +
131D ASP* 1.3 72.3 - - - +
133D ASP* 1.3 57.1 + - - +
135D LEU* 3.7 9.9 - - - +
136D MET* 2.9 42.2 + - + +
197D ASN* 4.9 4.2 + - - +
199D TYR* 3.7 24.8 - - + -
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Residues in contact with ASP 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D ASP* 3.3 15.4 + - - +
132D ASP* 1.3 78.2 - - - +
134D ARG* 1.3 61.9 + - - +
136D MET* 3.5 2.8 + - - +
137D ASN* 3.2 29.4 + - - +
198D LYS* 3.2 17.6 + - - -
199D TYR* 2.4 39.4 + - - -
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Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLU* 3.0 22.2 + - - -
33D GLN* 3.3 24.7 + - - +
34D ASN* 3.0 26.1 + - - -
37D ILE* 3.5 29.8 - - + +
130D VAL* 3.6 21.5 - - + +
131D ASP* 3.0 18.0 + - - +
133D ASP* 1.3 73.7 - - - +
135D LEU* 1.3 60.3 + - - +
137D ASN* 3.2 13.6 + - + +
138D VAL* 2.9 33.3 + - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU* 4.0 13.9 - - + -
74D HIS* 3.8 29.8 - - + -
120D VAL* 5.4 1.1 - - + -
122D VAL* 4.2 19.5 - - + -
125D ILE* 4.2 24.2 - - + -
126D ARG* 3.9 20.0 - - + +
130D VAL* 3.8 11.8 - - + +
131D ASP 3.0 16.4 + - - +
132D ASP* 3.7 11.2 - - - +
134D ARG* 1.3 74.9 - - - +
136D MET* 1.3 64.5 + - - +
138D VAL* 3.1 16.8 + - + +
139D ILE* 3.1 20.9 + - + +
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Residues in contact with MET 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU* 4.3 10.3 - - + -
75D ASN* 3.9 10.3 - - - +
132D ASP* 2.9 22.2 + - + +
133D ASP 3.7 4.0 - - - +
135D LEU* 1.3 78.2 - - - +
137D ASN* 1.3 61.2 + - - +
139D ILE* 3.0 21.0 + - - +
140D SER* 3.0 19.1 + - - -
162D SER* 3.5 46.4 - - - +
163D ILE* 4.5 1.3 - - - +
165D TYR* 5.8 0.2 - - + -
166D PRO* 3.4 27.7 - - + +
169D ARG* 3.8 8.3 - - - +
199D TYR* 3.6 39.0 - - + +
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Residues in contact with ASN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ASP* 3.2 23.2 + - - +
134D ARG* 3.2 15.5 + - + +
136D MET* 1.3 74.4 - - - +
138D VAL* 1.3 57.8 + - + +
140D SER* 3.3 4.3 + - - -
141D GLU* 2.9 34.8 + - + +
169D ARG* 3.1 26.9 + - - +
199D TYR* 5.5 0.9 + - - -
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ILE* 3.8 36.1 - - + -
40D SER* 5.3 3.1 - - - -
41D LEU* 3.9 19.7 - - + +
120D VAL* 4.5 9.0 - - + -
125D ILE* 3.9 25.4 - - + -
134D ARG* 2.9 25.1 + - + +
135D LEU* 3.3 11.4 - - + +
137D ASN* 1.3 76.7 - - + +
139D ILE* 1.3 53.9 + - - +
141D GLU* 3.3 8.0 + - - +
142D SER* 2.8 41.0 + - - +
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 5.9 0.2 - - + -
70D VAL* 3.5 39.9 - - + -
72D LEU* 3.9 22.0 - - + -
120D VAL* 4.5 14.4 - - + -
122D VAL* 5.0 0.4 - - + -
135D LEU* 3.1 19.0 + - + +
136D MET* 3.0 21.8 + - - +
138D VAL* 1.3 72.7 - - - +
140D SER* 1.3 67.6 - - - +
142D SER* 3.0 17.5 + - - -
143D VAL* 3.0 18.9 + - + +
163D ILE* 4.7 3.6 - - + +
166D PRO* 3.9 18.2 - - + -
167D VAL* 4.2 19.3 - - + +
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Residues in contact with SER 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D MET 3.0 5.3 + - - -
137D ASN* 3.5 9.2 - - - -
139D ILE* 1.3 77.1 - - - +
141D GLU* 1.3 66.2 + - - +
143D VAL* 3.3 1.7 + - - -
144D LYS* 3.2 22.5 + - - +
166D PRO* 2.7 27.8 + - - +
169D ARG* 2.9 36.0 + - - -
170D ALA* 3.3 19.9 - - - +
173D GLU* 5.5 1.3 - - - -
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Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 3.9 23.6 - - + -
137D ASN* 2.9 24.5 + - + +
138D VAL* 3.6 7.0 - - - +
139D ILE 3.2 0.2 - - - -
140D SER* 1.3 79.1 - - - +
142D SER* 1.3 61.2 + - - +
144D LYS* 3.3 27.5 + - - +
145D LEU* 3.1 32.8 + - + +
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 3.4 12.5 - - - +
44D ILE* 4.1 14.8 - - - +
68D LEU* 3.8 9.5 - - - +
120D VAL* 3.7 30.5 - - - +
138D VAL* 2.8 25.7 + - - +
139D ILE 3.0 5.6 + - - -
141D GLU* 1.3 72.9 - - - +
143D VAL* 1.3 65.3 + - - +
145D LEU* 3.2 25.4 - - - +
146D VAL* 3.3 13.0 + - - +
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Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 3.8 18.4 - - + -
139D ILE* 3.0 14.7 + - + +
140D SER 3.3 7.6 + - - +
142D SER* 1.3 76.8 - - - +
144D LYS* 1.3 62.7 + - - +
146D VAL* 3.1 9.3 + - - +
147D MET* 3.0 24.2 + - - +
154D PRO* 4.0 24.0 - - + -
156D VAL* 4.4 3.8 - - + -
167D VAL* 4.1 34.5 - - + +
170D ALA* 3.9 15.3 - - + -
171D VAL* 4.1 13.9 - - + -
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Residues in contact with LYS 144 (chain D).
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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140D SER* 3.2 14.1 + - - +
141D GLU* 3.3 31.6 + - - +
143D VAL* 1.3 76.3 - - - +
145D LEU* 1.3 53.5 + - + +
147D MET* 3.1 9.6 + - - +
148D GLU* 2.7 53.4 + - - +
170D ALA* 3.8 32.5 - - + +
173D GLU* 2.9 37.1 + - - +
174D LYS* 4.6 17.5 + - + +
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 3.7 44.2 - - + +
44D ILE* 4.1 10.8 - - + -
45D ARG* 4.0 41.3 - - + +
48D ALA* 4.1 5.4 - - + +
141D GLU* 3.1 23.7 + - + +
142D SER* 3.2 13.0 - - - +
144D LYS* 1.3 75.1 - - + +
146D VAL* 1.3 66.3 + - - +
148D GLU* 3.5 25.8 + - - +
149D GLU* 3.7 16.1 + - - +
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Residues in contact with VAL 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ILE* 4.9 2.5 - - + -
48D ALA* 4.6 6.7 - - + -
66D SER* 4.0 16.2 - - - +
68D LEU* 4.5 14.8 - - + -
117D VAL* 3.9 31.2 - - + -
142D SER 3.6 13.2 - - - +
143D VAL* 3.1 8.6 + - - +
145D LEU* 1.3 77.2 - - - +
147D MET* 1.3 62.0 + - - +
149D GLU* 3.0 24.3 + - - +
152D LEU* 3.8 23.6 - - + +
153D ARG 4.3 0.2 - - - -
154D PRO* 4.2 24.5 - - + -
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Residues in contact with MET 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D VAL* 3.0 24.1 + - - +
144D LYS* 3.1 9.4 + - - +
146D VAL* 1.3 74.5 - - - +
148D GLU* 1.3 59.7 + - - +
149D GLU 3.2 6.9 + - - +
150D GLU* 4.3 11.8 - - - +
152D LEU 4.2 11.5 - - - +
154D PRO* 3.9 17.9 - - + -
170D ALA 4.2 1.6 - - - +
171D VAL* 3.8 32.3 - - + +
174D LYS* 3.6 45.3 - - + -
175D LEU* 4.0 28.7 - - + -
307D VAL* 5.0 6.3 - - + +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LYS* 2.7 35.4 + - - +
145D LEU* 3.9 23.6 - - - +
146D VAL 3.1 0.6 - - - -
147D MET* 1.3 72.2 - - - +
149D GLU* 1.3 62.9 + - + +
150D GLU* 3.6 8.3 + - - +
174D LYS* 2.9 33.2 + - - +
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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
------------------------------------------------------------
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