Contacts of the helix formed by residues 128 - 142 (chain A) in PDB entry 2VUU
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 TRP 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A MET* 3.2 49.0 - - + +
114A PRO* 3.3 14.4 - - + +
116A HIS* 3.6 22.9 - + - -
125A VAL* 2.9 30.9 + - + +
126A PRO 3.5 0.4 - - - -
127A MET* 1.3 94.9 - - + +
129A ALA* 1.3 68.4 + - - +
130A PRO* 3.3 2.7 - - - +
131A LYS* 2.9 18.5 + - - +
152A ILE* 5.3 2.2 - - + -
261A GLN* 4.0 17.5 - - - +
265A ILE* 5.0 4.5 - - + -
269A PHE* 3.3 38.4 - + - -
276A TYR* 3.6 33.2 - + - -
1353A NAP 3.7 19.1 + + - -
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Residues in contact with ALA 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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114A PRO 3.2 9.5 + - - +
115A ASP* 3.6 35.8 - - - +
124A ALA* 3.7 18.6 - - + -
125A VAL 3.1 10.3 + - - +
126A PRO* 5.6 0.4 - - + -
128A TRP* 1.3 79.8 - - - +
130A PRO* 1.3 67.8 - - + +
132A PHE* 3.1 18.4 + - - +
133A THR* 3.6 8.0 + - - -
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Residues in contact with PRO 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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88A GLU* 4.6 15.9 - - + +
89A ILE* 3.4 43.6 - - + +
126A PRO* 3.5 27.6 - - + +
127A MET* 4.2 1.8 - - - -
128A TRP 3.3 7.0 - - - +
129A ALA* 1.3 95.0 - - + +
131A LYS* 1.3 62.9 + - + +
133A THR* 3.2 11.8 + - - +
134A VAL* 3.4 3.7 + - - +
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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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80A ASN* 3.2 19.9 + - - -
81A THR* 3.1 24.0 + - - +
88A GLU* 3.0 33.2 + - - +
110A TYR* 3.5 21.0 + - - +
111A SER 3.7 11.9 + - - +
112A SER* 3.9 6.6 + - - -
113A MET* 3.7 35.4 - - + +
127A MET 4.0 11.0 - - - +
128A TRP 2.9 7.9 + - - +
130A PRO* 1.3 78.7 - - - +
132A PHE* 1.3 63.8 + - - +
134A VAL* 2.9 15.3 + - - +
135A GLU 3.0 9.9 + - - -
1353A NAP 3.1 24.5 - - - -
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Residues in contact with PHE 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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112A SER* 3.8 4.3 - - - -
113A MET 3.4 18.7 + - - +
114A PRO* 5.1 0.7 - - + -
115A ASP* 4.1 11.0 - - + -
118A LEU* 3.8 25.6 - - + -
119A TYR* 3.4 24.9 - + - -
129A ALA 3.1 12.2 + - - +
131A LYS* 1.3 79.1 - - - +
133A THR* 1.3 61.1 + - - +
135A GLU* 3.4 10.2 - - - +
136A ASN* 3.4 22.5 + - + +
149A TYR* 3.5 24.2 - + - -
215A ARG* 3.3 35.0 - - - -
279A LEU* 4.7 4.0 - - + -
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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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89A ILE* 3.7 30.1 - - + +
93A LYS* 5.8 4.7 - - - -
115A ASP* 5.2 4.0 + - - -
129A ALA 3.6 8.5 + - - -
130A PRO* 3.2 11.2 + - - +
131A LYS 3.1 0.4 - - - -
132A PHE* 1.3 76.8 - - - +
134A VAL* 1.3 65.5 + - - +
136A ASN* 3.5 11.6 + - - +
137A TYR* 3.3 19.3 + - + +
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Residues in contact with VAL 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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88A GLU 3.6 22.4 - - - +
89A ILE* 3.7 18.6 - - + +
92A GLY* 3.3 36.8 - - - +
93A LYS* 4.1 2.5 - - + +
108A TYR* 5.9 0.2 - - - +
110A TYR* 3.4 29.4 - - + +
130A PRO 3.5 14.6 - - - +
131A LYS* 2.9 2.6 + - - +
133A THR* 1.3 74.3 - - - +
135A GLU* 1.3 66.1 + - - +
137A TYR* 3.1 8.2 + - + +
138A VAL* 2.9 27.4 + - + +
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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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110A TYR* 4.0 3.3 - - + -
112A SER* 2.9 21.6 + - - +
131A LYS 3.0 6.2 + - - +
132A PHE* 3.4 14.5 - - + +
134A VAL* 1.3 76.3 - - - +
136A ASN* 1.3 64.2 + - - +
138A VAL* 3.0 15.1 + - - +
139A ARG* 2.8 32.0 + - - +
147A PHE* 3.3 37.8 - - + -
149A TYR* 2.6 24.2 + - - -
215A ARG* 2.7 36.5 + - - +
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Residues in contact with ASN 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 PHE* 3.4 11.5 + - + +
133A THR* 3.6 13.3 + - - +
135A GLU* 1.3 80.8 - - - +
137A TYR* 1.3 58.3 + - - +
139A ARG* 3.4 16.8 + - - +
140A GLN* 2.9 40.4 + - - +
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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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92A GLY 4.8 0.9 - - - -
93A LYS* 3.5 64.5 - - + +
96A ALA* 4.1 5.4 - - + -
97A ASP* 2.6 36.4 + - - -
133A THR 3.3 10.5 + - - +
134A VAL* 3.1 12.9 + - - +
135A GLU 3.1 0.6 - - - -
136A ASN* 1.3 77.4 - - - +
138A VAL* 1.3 66.1 + - - +
140A GLN* 3.1 32.1 - - - +
141A LEU* 3.0 48.0 + - + +
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Residues in contact with VAL 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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96A ALA* 4.0 18.4 - - + -
108A TYR* 3.9 31.0 - - + +
110A TYR* 4.9 2.9 - - + -
134A VAL* 2.9 26.4 + - + +
135A GLU* 3.0 7.8 + - - +
137A TYR* 1.3 75.2 - - - +
139A ARG* 1.3 63.6 + - - +
141A LEU* 3.2 15.0 + - - +
142A GLY 3.3 8.0 + - - -
143A LEU* 3.5 16.7 + - + -
145A SER* 3.4 29.6 - - - +
147A PHE* 3.6 14.8 - - + -
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Residues in contact with ARG 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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135A GLU* 2.8 46.7 + - - +
136A ASN* 3.4 18.4 - - - +
138A VAL* 1.3 77.3 - - - +
140A GLN* 1.3 62.5 + - - +
142A GLY* 3.1 14.9 + - - -
143A LEU 5.3 0.9 - - - +
145A SER* 4.9 3.8 - - - +
147A PHE* 3.7 16.8 - - + -
213A GLY* 2.9 42.2 + - - -
215A ARG* 3.2 30.4 - - - +
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Residues in contact with GLN 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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100A LYS* 5.3 0.3 + - - -
136A ASN* 2.9 28.3 + - - +
137A TYR* 3.1 38.2 - - + +
139A ARG* 1.3 78.3 - - - +
141A LEU* 1.3 62.9 + - + +
142A GLY* 3.1 1.8 + - - -
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Residues in contact with LEU 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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96A ALA* 3.5 31.4 - - + +
97A ASP* 3.4 21.3 - - - +
100A LYS* 3.0 46.9 + - + +
137A TYR* 3.0 46.0 + - + +
138A VAL 3.2 7.6 + - - +
140A GLN* 1.3 77.6 - - + +
142A GLY* 1.3 60.9 + - - +
143A LEU* 3.6 12.4 + - + +
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Residues in contact with GLY 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 VAL 3.3 0.2 + - - -
139A ARG 3.1 13.4 + - - -
140A GLN 3.1 5.6 - - - -
141A LEU* 1.3 79.9 - - - +
143A LEU* 1.3 66.7 + - - +
144A PRO* 3.4 6.1 - - - +
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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