Contacts of the helix formed by residues 119 - 130 (chain A) in PDB entry 3V50
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 VAL 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A VAL* 3.5 31.4 - - + -
89A GLU* 3.7 29.6 - - + +
90A GLN 3.5 13.9 - - - +
91A LEU* 3.4 8.5 + - + -
93A ARG* 2.9 22.6 + - - +
95A ILE* 3.8 24.0 - - + -
117A MET 3.9 0.2 + - - -
118A THR* 1.3 73.2 - - - +
120A GLY* 1.3 63.4 + - - +
122A LEU* 3.1 11.6 + - + +
123A CYS* 3.0 19.6 + - - +
138A LEU* 3.9 10.7 - - + +
141A THR* 5.4 1.3 - - + +
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Residues in contact with GLY 120 (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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91A LEU* 2.8 38.5 + - - -
118A THR* 4.0 0.7 - - - -
119A VAL* 1.3 78.8 - - - +
121A GLU* 1.3 56.6 + - - +
123A CYS* 3.3 3.3 + - - +
124A ALA* 3.0 28.2 + - - +
210A TRP* 3.7 12.6 + - - -
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Residues in contact with GLU 121 (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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94A LYS* 4.8 3.1 - - - +
112A HIS* 5.3 8.8 + - - -
116A GLY 4.5 1.6 - - - +
117A MET* 3.4 25.2 - - + +
118A THR* 2.9 46.2 + - + +
120A GLY* 1.3 76.3 - - - +
122A LEU* 1.3 58.1 + - - +
124A ALA* 3.3 6.9 + - - +
125A ALA* 2.8 30.8 + - - +
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Residues in contact with LEU 122 (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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95A ILE* 3.9 31.2 - - + -
97A TYR* 4.9 0.7 - - + -
109A SER* 5.2 0.4 - - - -
117A MET* 3.8 35.7 - - + +
118A THR 2.8 18.6 + - - +
119A VAL* 3.1 11.0 + - - +
121A GLU* 1.3 78.1 - - - +
123A CYS* 1.3 58.3 + - - +
125A ALA 3.2 0.3 + - - -
126A ALA* 2.9 30.1 + - - +
134A ALA* 3.5 29.7 - - + +
137A LEU* 3.9 26.5 - - + -
138A LEU* 3.7 19.5 - - + -
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Residues in contact with CYS 123 (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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77A CYS* 2.1 51.8 - - - -
80A VAL* 4.2 11.2 - - - -
119A VAL 3.0 11.0 + - - +
120A GLY 3.3 1.5 + - - +
122A LEU* 1.3 76.8 - - - +
124A ALA* 1.3 62.4 + - - +
126A ALA* 4.5 0.4 - - - -
127A ILE* 2.9 30.5 + - - +
138A LEU* 3.7 18.8 - - - -
210A TRP* 3.3 33.2 - - + -
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Residues in contact with ALA 124 (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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120A GLY 3.0 17.3 + - - +
121A GLU* 3.6 8.3 - - - +
123A CYS* 1.3 76.8 - - - +
125A ALA* 1.3 56.4 + - - +
128A THR* 2.6 45.9 + - + +
210A TRP* 3.7 25.0 - - + +
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Residues in contact with ALA 125 (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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108A VAL* 3.8 30.7 - - + -
117A MET* 3.9 11.0 - - + -
121A GLU 2.8 20.8 + - - +
122A LEU 3.7 4.0 - - - +
124A ALA* 1.3 73.1 - - - +
126A ALA* 1.3 64.0 + - - +
129A MET* 3.1 24.1 + - - +
130A GLY 3.2 0.2 + - - -
131A ASP* 3.0 25.7 + - + -
134A ALA* 4.1 3.1 - - + -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LYS* 3.4 27.7 - - + +
76A LEU* 5.4 0.4 - - + -
77A CYS* 5.1 1.8 - - - -
122A LEU 2.9 17.0 + - - +
123A CYS* 3.8 3.4 - - - +
125A ALA* 1.3 77.2 - - - +
127A ILE* 1.3 60.2 + - + +
130A GLY* 3.2 23.7 + - - -
131A ASP 3.6 19.7 - - - +
134A ALA* 4.1 0.8 - - - +
135A ALA* 4.1 16.8 - - + +
138A LEU* 4.3 8.5 - - + -
234A LYS* 3.8 1.7 - - - -
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Residues in contact with ILE 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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73A LYS* 3.9 23.3 - - + +
74A VAL* 4.2 17.3 - - + +
77A CYS* 3.7 32.1 - - + -
123A CYS 2.9 13.9 + - - +
126A ALA* 1.3 78.6 - - + +
128A THR* 1.3 61.1 + - - +
130A GLY 4.4 0.5 + - - -
207A LEU* 4.3 5.4 - - + +
210A TRP* 3.6 49.1 - - + +
211A MET* 4.2 7.9 - - + +
214A ASP* 3.5 10.4 - - - +
233A ASP 5.0 2.0 - - - +
234A LYS* 3.4 28.6 + - + +
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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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124A ALA* 2.6 40.2 + - + +
127A ILE* 1.3 74.8 - - + +
129A MET* 1.3 70.1 + - - +
130A GLY 3.7 0.2 - - - -
210A TRP* 3.3 33.9 - - + +
213A ASP* 3.4 28.7 - - + +
214A ASP* 3.4 9.3 - - - +
215A ARG* 2.7 33.8 + - - +
216A VAL 3.6 1.6 + - - -
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Residues in contact with MET 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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105A TYR* 3.5 18.0 + - - -
107A PRO* 3.9 7.3 - - + +
108A VAL* 3.8 28.9 - - + -
125A ALA* 3.1 15.1 + - - +
128A THR* 1.3 92.5 + - - +
130A GLY* 1.3 65.8 + - - +
131A ASP 3.2 1.8 + - - +
215A ARG* 3.8 27.8 - - + +
216A VAL* 3.7 12.7 - - - +
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Residues in contact with GLY 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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73A LYS* 3.1 11.4 + - - -
105A TYR* 3.3 9.8 - - - -
125A ALA 3.2 2.2 + - - -
126A ALA 3.2 9.4 + - - -
127A ILE 4.4 1.0 + - - -
128A THR 3.7 1.2 - - - -
129A MET* 1.3 78.0 - - - +
131A ASP* 1.3 64.2 + - - +
132A ASN* 3.2 3.5 + - - +
216A VAL* 3.9 4.7 - - - +
234A LYS* 4.6 1.1 - - - -
301A SA2 3.1 43.2 - - - +
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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