Contacts of the strand formed by residues 146 - 157 (chain C) in PDB entry 1VHA
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 GLY 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.0 7.5 - - - +
11C HIS 3.2 15.0 - - - -
13C PHE* 3.5 14.4 - - - -
101C ALA* 5.4 0.2 - - - -
102C GLN 5.5 0.3 + - - -
140C PHE* 3.8 3.6 + - - -
141C THR* 3.6 23.3 - - - +
144C GLN* 3.3 2.4 - - - -
145C GLU* 1.3 83.3 + - - +
147C ILE* 1.3 70.3 + - - +
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 3.3 5.7 - - - +
11C HIS* 2.9 43.1 + - + +
13C PHE* 3.8 19.3 - - + -
38C GLY 4.9 4.5 - - - +
40C VAL* 3.8 28.9 - - + +
99C ILE* 5.6 3.8 - - + -
100C ILE 3.7 8.1 - - - +
101C ALA* 3.6 25.4 - - + -
102C GLN 5.2 1.1 - - - +
106C MSE 6.2 2.7 - - + -
140C PHE* 4.8 0.6 - - - -
141C THR* 4.0 3.8 - - - -
146C GLY* 1.3 80.0 - - - +
148C ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PHE* 4.2 13.9 - - + -
9C ASP 3.2 11.4 - - - +
10C VAL* 4.1 12.6 - - + -
40C VAL* 4.0 4.4 - - - +
99C ILE* 3.7 5.9 - - - +
100C ILE* 2.7 46.1 + - + +
140C PHE* 4.4 4.7 - - + -
141C THR* 4.0 11.4 - - + +
147C ILE* 1.3 76.0 - - - +
149C CYS* 1.3 61.5 + - - +
170C ACY 4.9 2.5 - - + -
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Residues in contact with CYS 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PHE* 3.3 11.9 - - - -
9C ASP 2.9 30.1 + - - +
40C VAL* 3.5 28.9 - - + +
41C ALA* 3.6 16.8 - - - -
44C ALA* 3.7 6.5 - - - +
97C ILE* 3.4 33.2 - - - -
98C THR 3.4 11.0 - - - -
99C ILE* 4.0 4.7 - - - -
100C ILE* 4.8 1.6 - - - -
148C ALA* 1.3 79.5 - - - +
150C GLU* 1.3 67.5 + - - +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 2.8 15.3 - - - +
6B HIS* 3.0 36.6 + - + +
8B PHE* 5.0 2.3 - - - -
150B GLU* 2.5 24.5 - - - +
6C HIS* 2.5 33.4 + - + +
7C GLY 3.5 2.2 - - - +
8C PHE* 4.2 12.4 - - - -
96C ASP 4.3 0.2 - - - +
97C ILE* 3.6 0.2 - - - -
98C THR* 2.8 37.6 + - - +
100C ILE* 4.5 13.8 - - + +
149C CYS* 1.3 78.7 - - - +
151C ALA* 1.3 64.9 + - - +
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Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B HIS* 5.8 0.7 - - - -
6C HIS* 3.3 5.9 - - - -
7C GLY 2.7 37.4 + - - +
44C ALA* 3.6 34.5 - - + +
45C LEU* 3.7 11.0 - - + +
48C ALA* 4.1 2.7 - - + -
96C ASP 3.6 5.4 - - - -
97C ILE* 4.2 13.7 - - + -
150C GLU* 1.3 79.1 - - - +
152C VAL* 1.3 66.2 + - - +
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A VAL* 4.8 10.8 - - + -
4B ILE* 4.0 31.9 - - + -
5B GLY 4.3 1.1 - - - -
6B HIS* 3.8 37.5 - - + -
152B VAL* 5.0 5.4 - - + -
5C GLY 3.0 11.9 - - - +
6C HIS* 4.5 9.9 - - + -
45C LEU* 5.2 1.0 - - - +
48C ALA* 4.2 1.6 - - - -
95C VAL* 3.6 3.5 - - - +
96C ASP* 3.1 42.4 + - + +
151C ALA* 1.3 80.0 - - - +
153C ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.3 3.6 - - - -
3C ARG 3.6 0.5 - - - +
4C ILE* 3.4 7.8 - - - +
5C GLY 2.8 30.6 + - - -
45C LEU* 5.2 0.7 - - + -
48C ALA* 3.9 28.5 - - + +
49C ILE* 4.1 11.2 - - + +
52C ALA* 4.6 0.8 - - - +
94C ASN 3.8 4.5 - - - -
95C VAL* 3.9 16.4 - - + -
152C VAL* 1.3 77.3 - - - +
154C LEU* 1.3 63.5 + - - +
155C LEU* 4.0 5.6 - - + -
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Residues in contact with LEU 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU* 4.7 7.6 - - + -
2B ILE* 3.4 44.2 - - + +
3B ARG* 4.2 0.7 - - - -
4B ILE* 3.6 23.8 - - + +
154B LEU* 4.9 3.1 - - + -
2C ILE* 3.6 27.1 - - + -
3C ARG 3.3 13.7 - - - +
4C ILE* 4.6 4.7 - - + -
92C ILE* 4.2 0.7 - - - +
93C GLY* 2.7 35.8 + - - -
94C ASN* 3.0 32.7 + - - +
95C VAL* 5.5 0.3 - - - +
153C ALA* 1.3 75.1 - - - +
155C LEU* 1.3 58.4 + - - +
156C ILE* 5.0 2.0 - - + -
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.3 6.6 - - - +
3C ARG* 2.7 43.3 + - + +
49C ILE* 3.5 31.0 - - + +
52C ALA* 3.6 20.4 - - + -
53C ALA* 4.1 7.0 - - + +
85C VAL* 3.1 35.7 - - + -
90C TYR* 3.9 17.6 - - + -
91C LYS 3.6 11.7 - - - +
92C ILE* 4.2 20.4 - - + -
153C ALA* 5.0 3.4 - - + -
154C LEU* 1.3 78.4 - - - +
156C ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B SER* 5.2 9.6 - - - -
1B LEU 6.2 0.2 - - - +
2B ILE* 4.5 21.5 - - + +
1C LEU 3.7 10.8 - - - +
2C ILE* 4.8 9.2 - - + -
90C TYR* 3.5 6.0 - - - -
91C LYS* 2.9 45.9 + - + +
92C ILE 5.1 0.2 - - - +
93C GLY* 3.6 25.1 - - - -
154C LEU* 4.8 3.6 - - + +
155C LEU* 1.3 79.2 - - - +
157C ARG* 1.3 76.9 + - + +
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Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C SER* 3.6 19.8 + - - +
1C LEU* 3.2 28.2 + - + +
88C LYS* 3.1 23.9 + - - +
89C GLY* 3.5 10.3 + - - +
90C TYR* 3.1 37.8 + - - -
91C LYS* 4.4 3.0 - - - +
156C ILE* 1.3 84.2 - - + +
158C GLN* 1.3 68.0 + - - +
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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