Contacts of the helix formed by residues 120 - 130 (chain A) in PDB entry 3A33
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 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A HIS 4.1 5.2 - - - +
76A PRO 3.1 7.3 + - - +
78A ILE 3.6 26.2 - - - +
79A ASN* 3.8 20.2 - - + -
118A PRO* 4.2 2.7 - - - -
119A LEU* 1.3 82.2 - - + +
121A PRO* 1.4 65.5 - - - +
122A GLU* 3.4 24.2 - - - +
123A ILE* 3.0 37.5 + - + +
124A ALA* 3.3 10.0 + - - +
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Residues in contact with PRO 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 4.0 24.8 - - + +
119A LEU 3.3 13.2 - - - +
120A VAL* 1.4 83.1 - - - +
122A GLU* 1.3 70.4 + - + +
124A ALA* 3.2 2.9 + - - +
125A ARG* 2.9 29.4 + - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 5.3 0.2 - - - -
120A VAL* 3.4 19.8 - - + +
121A PRO* 1.3 94.3 - - + +
123A ILE* 1.3 63.5 + - + +
125A ARG* 3.7 15.8 + - - +
126A ILE* 3.2 24.8 + - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE 5.7 0.7 - - - +
74A TYR* 3.6 57.0 - - + +
75A HIS 3.8 18.4 - - - +
76A PRO* 3.5 30.3 - - + -
78A ILE 5.1 1.3 - - - +
120A VAL* 3.0 31.8 + - + +
122A GLU* 1.3 76.5 - - + +
124A ALA* 1.3 61.4 + - - +
126A ILE* 3.1 5.7 + - - +
127A TYR* 2.8 24.9 + - - +
134A TYR* 3.7 4.3 - - + -
141A TRP* 6.0 2.2 - - + -
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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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76A PRO* 3.9 10.4 - - + +
115A PRO* 3.3 32.3 - - + +
118A PRO* 3.5 24.0 - - + -
120A VAL 3.3 2.4 + - - +
121A PRO* 3.2 8.5 + - + +
123A ILE* 1.3 79.1 - - - +
125A ARG* 1.3 56.3 + - - +
127A TYR* 3.2 5.8 + - - +
128A LYS* 2.8 38.7 + - - +
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Residues in contact with ARG 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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121A PRO 2.9 15.6 + - - +
122A GLU* 3.7 15.5 + - - +
124A ALA* 1.3 76.4 - - - +
126A ILE* 1.3 76.0 + - - +
128A LYS* 3.4 10.0 + - - +
129A THR* 2.7 54.6 + - + +
133A LYS* 5.6 2.6 - - - +
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Residues in contact with ILE 126 (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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74A TYR* 4.0 16.8 - - - +
122A GLU 3.2 18.8 - - - +
123A ILE 3.1 5.9 + - - +
125A ARG* 1.3 94.5 - - - +
127A TYR* 1.3 67.5 + - - +
129A THR* 3.9 5.4 - - - -
130A ASP* 2.8 35.8 + - + +
133A LYS* 3.7 43.1 - - + +
134A TYR* 3.9 20.9 - - + +
137A ILE* 4.9 2.5 - - + -
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Residues in contact with TYR 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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76A PRO* 4.7 3.8 - - + -
111A CYS 5.3 0.7 + - - -
112A ASP* 5.0 2.9 + - - -
113A PRO* 3.7 38.1 + - + +
115A PRO* 3.5 35.4 - - + -
123A ILE 2.8 13.2 + - - +
124A ALA* 3.4 13.2 - - - +
126A ILE* 1.3 78.8 - - - +
128A LYS* 1.3 60.6 + - + +
131A ARG* 3.0 75.4 + - - +
134A TYR* 3.5 45.4 - + + +
135A ASN* 5.6 0.2 - - - -
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Residues in contact with LYS 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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115A PRO* 3.0 45.3 + - + -
116A ASP* 3.4 26.4 + - - +
118A PRO* 5.3 2.0 - - - +
124A ALA* 2.8 24.3 + - - +
125A ARG* 3.9 8.1 - - - +
127A TYR* 1.3 79.9 - - + +
129A THR* 1.3 62.7 - - + +
131A ARG* 5.2 4.2 + - - +
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Residues in contact with THR 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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125A ARG* 2.7 39.7 + - + +
126A ILE* 3.9 4.0 - - - -
128A LYS* 1.3 82.9 - - + +
130A ASP* 1.3 67.4 + - - +
131A ARG 4.0 0.7 - - - -
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Residues in contact with ASP 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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126A ILE* 2.8 17.8 + - + +
129A THR* 1.3 85.0 + - - +
131A ARG* 1.3 65.5 + - - +
132A GLU* 3.0 15.5 + - - +
133A LYS* 2.9 49.7 + - + +
134A TYR 3.0 9.2 + - - -
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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