Contacts of the helix formed by residues 121 - 128 (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 PRO 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 4.3 14.6 - - + -
40D SER* 3.7 42.8 - - - +
43D LEU* 4.9 9.4 - - + -
44D ILE* 5.0 2.5 - - + -
71D PRO* 5.6 0.2 - - + -
119D ASP* 3.3 9.2 - - + +
120D VAL* 1.4 83.3 - - + +
122D VAL* 1.3 61.9 + - - +
123D GLN 3.5 2.0 - - - -
124D GLU* 3.4 26.7 - - + +
125D ILE* 3.2 26.1 + - - +
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Residues in contact with VAL 122 (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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70D VAL* 3.9 19.7 - - + -
71D PRO* 3.5 38.5 - - + +
72D LEU* 3.8 24.5 - - + -
120D VAL* 2.8 28.9 + - + +
121D PRO* 1.3 67.7 - - - +
123D GLN* 1.3 75.5 + - - +
124D GLU* 4.1 0.2 + - - -
125D ILE* 3.1 5.2 + - - +
126D ARG* 3.0 26.2 + - - +
135D LEU* 4.2 21.9 - - + +
139D ILE* 5.0 0.2 - - + -
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Residues in contact with GLN 123 (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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47A ARG* 4.4 1.3 + - - -
87A PRO* 6.5 0.9 - - + -
71D PRO* 2.9 32.5 + - + +
72D LEU* 4.2 4.9 - - - +
73D GLY 4.8 1.8 - - - +
74D HIS* 5.3 0.2 + - - -
83D ALA* 4.4 12.5 - - + +
121D PRO 3.5 0.4 - - - -
122D VAL* 1.3 86.7 - - - +
124D GLU* 1.3 66.1 + - - +
126D ARG* 3.2 33.1 + - - +
127D ASP* 3.0 29.6 + - - +
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Residues in contact with GLU 124 (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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43A LEU* 5.0 15.3 - - + -
47A ARG* 3.5 31.7 + - - +
117A VAL 5.3 0.7 - - - +
118A GLY* 4.5 4.8 - - - -
119A ASP* 3.7 31.3 + - - +
36D VAL* 4.6 12.6 - - + +
121D PRO* 3.4 35.8 - - + +
122D VAL 3.2 0.4 - - - -
123D GLN* 1.3 81.8 + - - +
125D ILE* 1.3 66.1 + - + +
127D ASP* 3.4 2.9 + - - +
128D CYS* 3.3 24.1 + - - +
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Residues in contact with ILE 125 (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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36D VAL* 4.5 7.2 - - + -
37D ILE* 4.4 12.1 - - + -
40D SER* 3.9 27.4 - - - +
120D VAL* 4.6 6.5 - - + -
121D PRO 3.2 20.2 - - - +
122D VAL 3.1 7.0 + - - +
124D GLU* 1.3 74.1 - - - +
126D ARG* 1.3 66.9 + - - +
128D CYS* 3.1 25.2 - - - -
130D VAL* 3.4 36.6 + - + +
135D LEU* 4.2 20.0 - - + -
138D VAL* 3.9 28.7 - - + -
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Residues in contact with ARG 126 (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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73D GLY 6.0 0.2 - - - +
74D HIS* 3.4 57.0 + - + +
80D GLN* 4.6 5.3 + - - -
122D VAL* 3.0 19.0 + - - +
123D GLN* 3.2 36.3 + - - +
125D ILE* 1.3 74.9 - - - +
127D ASP* 1.3 58.5 - - - +
129D GLY* 2.9 24.6 + - - -
130D VAL 3.8 10.6 + - - +
135D LEU* 3.9 17.5 - - + -
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Residues in contact with ASP 127 (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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47A ARG* 3.0 37.1 + - - +
51A LYS* 2.7 35.9 + - - -
116A ASP* 4.5 4.3 - - - +
123D GLN 3.0 16.5 + - - +
124D GLU 3.8 2.2 - - - +
125D ILE 3.3 0.4 - - - -
126D ARG* 1.3 80.6 - - - +
128D CYS* 1.3 59.6 + - - +
129D GLY* 3.4 1.7 + - - -
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Residues in contact with CYS 128 (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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47A ARG* 5.5 6.1 - - + -
50A LEU* 3.9 26.0 - - + +
51A LYS* 5.2 2.7 - - - +
29D ILE* 4.4 7.4 - - - +
33D GLN* 2.8 42.9 + - - +
36D VAL* 4.4 14.4 - - + -
37D ILE* 6.0 0.2 - - - -
124D GLU 3.3 12.2 + - - +
125D ILE* 3.1 24.7 - - - -
126D ARG 3.2 1.0 - - - -
127D ASP* 1.3 79.5 - - - +
129D GLY* 1.3 50.6 + - - +
130D VAL* 3.7 16.6 - - - -
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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