Contacts of the helix formed by residues 121 - 128 (chain B) 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 PRO 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B SER* 3.5 37.7 - - - +
43B LEU* 5.4 4.3 - - + -
44B ILE* 4.8 4.7 - - + -
71B PRO* 5.4 0.4 - - + -
119B ASP* 3.5 8.9 - - + +
120B VAL* 1.3 83.5 - - + +
122B VAL* 1.3 64.0 + - - +
123B GLN 3.4 2.5 - - - -
124B GLU* 3.4 18.6 + - - +
125B ILE* 3.2 27.0 + - - +
43E LEU* 4.0 14.6 - - + -
47E ARG* 4.3 12.1 - - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B VAL* 4.1 15.7 - - + -
71B PRO* 3.5 26.1 - - + +
72B LEU* 3.9 22.2 - - + -
120B VAL* 2.7 36.8 + - + +
121B PRO* 1.3 68.3 - - - +
123B GLN* 1.3 86.7 + - - +
124B GLU 3.2 0.3 + - - -
125B ILE* 3.2 7.2 + - - +
126B ARG* 3.0 28.3 + - - +
135B LEU* 4.3 15.2 - - + +
139B ILE* 4.9 0.7 - - + -
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PRO* 2.9 33.0 + - + +
72B LEU* 4.2 5.5 - - - +
73B GLY 4.7 1.6 - - - +
74B HIS* 5.3 0.2 + - - -
83B ALA* 4.4 12.0 - - + +
121B PRO 3.4 0.8 - - - -
122B VAL* 1.3 89.2 - - - +
124B GLU* 1.3 62.7 + - - +
126B ARG* 2.9 36.9 + - - +
127B ASP* 2.9 33.9 + - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 4.6 1.2 - - + +
121B PRO* 3.6 25.9 - - - +
122B VAL 3.2 0.4 + - - -
123B GLN* 1.3 83.4 + - - +
125B ILE* 1.3 67.0 + - + +
127B ASP* 3.4 15.6 + - + +
128B CYS* 3.5 13.9 + - - +
47E ARG* 3.3 60.6 + - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 4.5 8.5 - - + -
37B ILE* 4.4 10.8 - - + -
40B SER* 3.8 25.8 - - - +
120B VAL* 4.6 3.8 - - + -
121B PRO 3.2 19.8 + - - +
122B VAL* 3.2 9.8 + - - +
124B GLU* 1.3 75.8 - - + +
126B ARG* 1.3 63.4 + - - +
128B CYS* 3.3 21.9 + - - -
130B VAL* 3.5 39.0 + - + +
135B LEU* 4.2 17.7 - - + -
138B VAL* 3.8 32.1 - - + -
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B HIS* 3.3 56.9 + - + +
80B GLN* 4.7 5.3 + - - -
122B VAL* 3.0 17.2 + - - +
123B GLN* 2.9 39.5 + - - +
125B ILE* 1.3 75.2 - - - +
127B ASP* 1.3 62.2 + - - +
129B GLY* 3.1 16.5 + - - -
130B VAL 4.1 10.6 + - - +
132B ASP* 5.9 0.2 - - - +
135B LEU* 3.9 18.8 - - + -
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLN 2.9 17.2 + - - +
124B GLU* 3.9 10.3 - - - +
125B ILE 3.2 0.8 - - - -
126B ARG* 1.3 75.6 - - - +
128B CYS* 1.3 58.5 + - - +
129B GLY 3.3 1.5 + - - -
51E LYS* 3.0 45.3 + - - +
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Residues in contact with CYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 5.4 0.7 - - - +
33B GLN* 3.0 29.8 + - - +
36B VAL* 4.2 26.0 - - + -
124B GLU 3.5 10.2 + - - +
125B ILE 3.3 18.0 + - - -
126B ARG 3.1 0.8 - - - -
127B ASP* 1.3 78.7 - - - +
129B GLY* 1.3 55.4 + - - +
130B VAL* 3.9 13.9 - - - -
47E ARG* 6.3 2.7 - - + -
50E LEU* 3.8 21.4 - - + +
51E LYS* 4.4 10.8 - - - +
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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