Contacts of the helix formed by residues 130 - 145 (chain D) in PDB entry 3VZC
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 THR 130 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLN 5.5 0.4 - - - -
129D VAL* 1.3 76.5 - - - +
131D ASN* 1.3 94.3 + - + +
132D GLU 3.2 0.5 + - - -
133D ASP* 3.2 21.0 + - - +
134D LEU* 3.4 4.6 + - - -
270D SER* 3.8 16.3 + - - -
271D GLU* 4.4 23.1 - - - +
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Residues in contact with ASN 131 (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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109D PRO* 4.8 4.2 - - - +
130D THR* 1.3 96.5 + - + +
132D GLU* 1.3 76.7 + - + +
134D LEU* 3.1 11.4 + - - +
135D LEU* 3.0 24.3 + - - +
190D MET* 5.1 13.1 - - - +
270D SER* 5.3 0.6 + - - -
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Residues in contact with GLU 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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33D LEU* 3.4 27.3 - - + +
37D HIS* 3.8 29.5 - - + +
130D THR 3.2 0.2 + - - -
131D ASN* 1.3 94.9 - - + +
133D ASP* 1.3 62.1 + - - +
135D LEU* 3.6 9.4 - - + +
136D THR* 2.9 34.7 + - - -
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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
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129D VAL* 3.6 26.0 - - + +
130D THR* 3.2 14.1 + - - +
132D GLU* 1.3 78.9 - - - +
134D LEU* 1.3 58.0 + - - +
136D THR* 3.6 4.6 + - - -
137D ASN* 3.1 33.3 + - - +
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Residues in contact with LEU 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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109D PRO* 3.8 25.4 - - + -
114D ASN* 4.4 5.8 - - + +
117D ALA* 4.1 4.5 - - + +
118D ALA* 4.2 14.1 - - - +
121D ASN* 3.5 37.9 - - + +
129D VAL* 3.7 29.1 - - + +
130D THR* 3.4 5.5 + - - -
131D ASN 3.1 11.6 + - - +
133D ASP* 1.3 78.2 - - - +
135D LEU* 1.3 58.8 + - - +
137D ASN* 3.8 1.3 - - - -
138D CYS* 2.9 41.3 + - - -
270D SER* 4.0 21.1 - - - -
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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
----------------------------------------------------------
33D LEU* 3.9 31.9 - - + +
37D HIS* 3.8 26.5 - - + -
38D VAL* 3.8 22.0 - - + -
78D MET* 3.8 14.8 - - + -
108D LEU* 4.2 6.5 - - + -
109D PRO* 3.5 37.6 - - + +
131D ASN 3.0 14.0 + - - +
132D GLU* 3.3 10.5 + - - +
134D LEU* 1.3 76.4 - - - +
136D THR* 1.3 53.9 + - - +
138D CYS* 3.9 0.5 - - - +
139D THR* 2.7 40.2 + - - +
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Residues in contact with THR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS* 3.6 25.0 + - - +
41D LEU* 4.3 15.2 - - + +
132D GLU 2.9 17.0 + - - -
133D ASP* 3.9 6.2 - - - -
135D LEU* 1.3 77.2 - - - +
137D ASN* 1.3 59.0 + - - +
139D THR* 3.3 6.1 + - - -
140D LEU* 2.8 45.4 + - + +
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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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121D ASN* 3.2 31.6 - - - +
126D TYR* 3.5 37.0 - - + +
127D GLU 5.4 0.2 - - - +
129D VAL* 3.3 24.0 - - - +
133D ASP 3.1 17.0 + - - +
134D LEU 3.4 3.3 + - - +
136D THR* 1.3 76.8 - - - +
138D CYS* 1.3 62.9 + - - +
140D LEU* 3.1 17.3 + - - +
141D LEU* 2.9 27.0 + - - +
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Residues in contact with CYS 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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106D CYS* 4.9 2.9 - - - -
107D SER 3.7 17.5 - - - +
108D LEU* 3.7 6.2 - - + +
109D PRO* 3.8 12.6 - - + -
117D ALA* 3.8 39.9 - - - -
120D LEU* 5.7 2.5 - - - -
121D ASN* 4.7 5.4 - - - -
134D LEU* 2.9 31.5 + - - +
135D LEU 4.0 0.2 - - - +
137D ASN* 1.3 72.4 - - - +
139D THR* 1.3 62.8 + - - +
141D LEU* 3.1 17.2 + - + +
142D LEU* 3.1 19.2 + - - +
362D VAL* 5.0 0.5 - - - +
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Residues in contact with THR 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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37D HIS 4.2 1.0 + - - -
38D VAL* 3.6 41.4 - - + +
41D LEU* 3.8 35.0 - - + -
42D LEU* 4.5 4.5 - - + -
108D LEU* 3.5 14.3 - - + +
135D LEU 2.7 24.0 + - - -
136D THR* 3.5 5.6 - - - -
138D CYS* 1.3 74.1 - - - +
140D LEU* 1.3 57.9 + - - +
142D LEU* 3.0 8.2 + - + +
143D CYS* 2.8 30.3 + - - -
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Residues in contact with LEU 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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41D LEU* 4.9 15.7 - - + -
126D TYR* 4.2 10.1 - - + +
136D THR* 2.8 40.7 + - + +
137D ASN* 3.1 21.5 + - - +
139D THR* 1.3 72.8 - - - +
141D LEU* 1.3 60.8 + - - +
143D CYS* 3.3 10.8 + - + +
144D ARG* 3.1 51.8 + - - +
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Residues in contact with LEU 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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120D LEU* 3.9 31.9 - - + +
121D ASN* 4.6 5.8 - - - +
124D ALA* 3.8 18.4 - - + -
126D TYR* 4.3 4.0 - - + -
137D ASN 2.9 18.9 + - - +
138D CYS* 3.1 16.4 + - - +
140D LEU* 1.3 74.1 - - - +
142D LEU* 1.3 64.0 + - - +
144D ARG* 3.1 25.2 + - + +
145D ARG* 3.0 19.8 + - - -
146D LEU 4.5 3.1 + - - +
362D VAL* 4.1 15.4 - - + +
363D SER* 4.2 15.6 + - - -
364D GLY* 3.5 24.9 - - - +
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Residues in contact with LEU 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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11D LEU* 4.0 22.2 - - + -
17D VAL* 4.8 8.3 - - + -
38D VAL* 5.5 0.2 - - + -
42D LEU* 4.0 28.7 - - + -
47D ILE* 3.5 14.1 - - + +
74D ALA* 5.5 0.4 - - + -
76D VAL* 3.9 23.6 - - + -
106D CYS* 3.9 28.0 - - + -
108D LEU* 4.4 13.0 - - + -
138D CYS 3.1 11.4 + - - +
139D THR* 3.0 12.2 + - - +
141D LEU* 1.3 75.9 - - - +
143D CYS* 1.3 60.9 + - - +
145D ARG* 3.4 13.5 + - - +
362D VAL* 3.8 13.9 - - + +
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Residues in contact with CYS 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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13D ARG* 4.7 3.5 + - - -
41D LEU* 3.6 43.7 - - - -
42D LEU* 4.2 11.9 - - - -
45D ALA* 3.8 15.4 - - + +
47D ILE* 4.0 6.3 - - - -
139D THR* 2.8 19.1 + - - +
140D LEU* 3.7 14.8 - - + +
141D LEU 3.2 0.4 - - - -
142D LEU* 1.3 76.9 - - - +
144D ARG* 1.3 61.1 + - + +
145D ARG* 3.4 22.9 + - - +
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Residues in contact with ARG 144 (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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10D VAL* 4.7 1.2 - - - +
126D TYR* 2.7 31.9 + - - -
140D LEU* 3.1 39.7 + - + +
141D LEU* 3.1 32.6 + - + +
143D CYS* 1.3 74.2 - - + +
145D ARG* 1.3 67.0 + - - +
146D LEU* 3.4 25.7 + - + +
364D GLY* 6.0 0.2 - - - -
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Residues in contact with ARG 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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10D VAL* 3.3 10.2 - - + -
11D LEU* 3.0 53.1 + - + +
12D PRO 2.8 20.8 + - - -
13D ARG* 3.6 34.1 - - - +
14D PRO* 3.8 0.6 - - - +
15D CYS* 3.6 13.3 - - - +
45D ALA* 2.8 33.1 + - - +
46D GLU 3.5 11.1 + - - -
47D ILE* 3.2 18.8 - - + +
141D LEU 3.0 9.4 + - - -
142D LEU* 3.7 12.1 - - - +
143D CYS 3.3 22.1 + - - +
144D ARG* 1.3 76.9 - - - +
146D LEU* 1.3 62.2 + - - +
147D LEU* 3.7 6.8 + - - +
362D VAL* 5.2 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