Contacts of the helix formed by residues 125 - 129 (chain A) in PDB entry 1VLP
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 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A MSE 3.7 14.4 - - + -
23A VAL* 3.5 24.5 - - + -
27A PHE* 4.0 30.5 - + + +
30A VAL* 2.8 35.0 + - + +
32A VAL* 3.6 26.8 - - + +
34A TYR* 3.0 28.7 + - - -
123A GLY 3.5 1.0 + - - -
124A SER* 1.3 70.7 + - - +
126A LYS* 1.3 56.8 + - - +
128A THR* 3.2 4.2 + - - -
129A ILE* 3.0 38.6 + - + +
233A GLU* 3.5 24.9 + - - -
234A TRP* 4.1 16.6 - + - -
237A GLY* 3.7 31.2 - - - -
238A VAL 4.5 0.2 - - - -
241A ILE* 4.6 3.6 - - + -
380A LEU* 4.8 4.4 - - + +
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 3.0 33.9 + - + +
23A VAL* 3.5 15.8 - - + +
24A PHE* 4.1 26.7 - - + -
27A PHE 5.1 0.8 + - - -
28A PRO* 2.6 41.1 + - + +
87A TYR* 3.4 28.5 + - - +
93A TYR* 5.1 3.1 + - - -
95A LEU* 6.0 0.5 - - - +
124A SER* 3.5 13.7 + - - +
125A TRP* 1.3 76.4 - - - +
127A ASP* 1.3 70.9 + - - +
129A ILE* 4.1 2.2 - - - +
130A LEU* 5.7 0.7 - - - +
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Residues in contact with ASP 127 (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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87A TYR* 4.6 3.3 + - - -
93A TYR* 6.0 1.2 - - - -
94A LYS 5.5 1.7 - - - +
95A LEU* 4.3 12.3 - - - +
96A HIS* 5.3 10.4 + - - -
100A GLN* 3.8 27.4 + - - +
124A SER* 3.0 27.2 + - - +
126A LYS* 1.3 92.1 + - - +
128A THR* 1.3 59.4 + - - +
130A LEU 5.4 0.7 - - - -
131A TYR* 3.4 19.4 + - - -
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Residues in contact with THR 128 (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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32A VAL* 2.9 26.3 - - - +
34A TYR* 3.5 16.7 - - - -
100A GLN* 3.4 27.1 - - + -
121A VAL* 4.2 7.9 - - + +
122A SER* 3.6 6.5 - - - +
123A GLY* 3.5 22.7 - - - +
124A SER 3.1 14.0 + - - +
125A TRP 3.2 2.3 + - - -
127A ASP* 1.3 77.4 - - - +
129A ILE* 1.3 68.0 + - - +
130A LEU 3.3 3.1 - - - -
131A TYR* 3.1 25.8 + - - +
132A GLU 4.6 1.0 + - - -
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Residues in contact with ILE 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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16A LYS* 2.7 44.7 + - - +
19A MSE 3.4 48.0 - - + -
20A HIS* 3.5 41.7 - - + +
23A VAL* 3.9 8.5 - - + -
34A TYR* 3.7 10.9 - - - +
125A TRP* 3.0 33.2 + - - +
126A LYS* 4.1 3.4 - - - +
128A THR* 1.3 77.4 + - - +
130A LEU* 1.3 62.1 + - + +
131A TYR 3.4 0.5 + - - -
132A GLU 4.1 0.9 + - - -
233A GLU* 3.6 6.7 - - - +
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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