Contacts of the helix formed by residues 117 - 130 (chain A) in PDB entry 6PAX
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ALA* 3.8 10.1 - - + -
97A TRP* 4.2 24.7 - - + +
100A ARG* 4.1 22.9 - - - +
115A PRO 3.9 0.6 + - - -
116A SER* 1.3 72.8 - - - +
118A SER* 1.3 58.0 + - - +
120A ILE* 3.1 10.9 + - - +
121A ASN* 2.9 45.9 + - - +
2004C T 4.2 19.7 - - + +
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Residues in contact with SER 118 (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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116A SER* 3.5 10.9 - - - -
117A VAL* 1.3 79.1 - - - +
119A SER* 1.3 56.8 + - - +
121A ASN* 3.2 8.4 + - - +
122A ARG* 2.8 29.6 + - - +
125A ARG* 5.0 1.4 + - - -
1021B G 3.7 15.2 + - - -
1022B C 3.5 30.0 + - - -
1023B A 5.6 1.3 - - - -
2006C T 4.4 8.6 + - - +
2007C G 4.9 0.5 + - - -
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Residues in contact with SER 119 (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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75A VAL* 4.4 3.6 - - - -
115A PRO* 4.2 7.9 - - - -
116A SER* 2.9 14.0 + - - -
118A SER* 1.3 75.8 - - - +
120A ILE* 1.3 53.3 + - - +
122A ARG* 3.0 35.0 + - - +
123A VAL* 2.7 41.9 + - - +
1020B T 3.3 8.1 - - - +
1021B G 2.4 31.4 + - - -
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Residues in contact with ILE 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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84A ILE* 4.5 13.0 - - + -
96A ALA* 3.6 29.6 - - + +
99A ILE* 4.1 16.2 - - + -
100A ARG* 3.6 42.6 - - + +
103A LEU* 5.3 2.0 - - + -
115A PRO* 3.9 19.5 - - + +
116A SER 2.9 17.7 + - - +
117A VAL* 3.1 12.8 + - - +
119A SER* 1.3 73.8 - - - +
121A ASN* 1.3 57.8 + - - +
123A VAL* 3.1 11.0 + - - +
124A LEU* 2.8 37.8 + - + +
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Residues in contact with ASN 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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96A ALA* 3.4 21.2 - - - +
117A VAL* 2.9 21.4 + - - +
118A SER* 3.8 7.9 - - - +
120A ILE* 1.3 75.8 - - - +
122A ARG* 1.3 53.1 + - - +
124A LEU* 3.2 17.1 + - - +
125A ARG* 2.7 43.8 + - - +
2004C T 3.1 58.8 + - + +
2005C G 3.8 12.6 + - - +
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Residues in contact with ARG 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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76A ALA* 5.0 1.6 - - - +
118A SER* 2.8 13.9 + - - +
119A SER* 3.0 41.1 + - - +
121A ASN* 1.3 72.5 - - - +
123A VAL* 1.3 64.7 + - - +
125A ARG* 3.1 26.5 + - - +
126A ASN* 2.8 55.5 + - - +
1019B G 3.9 8.3 - - - +
1020B T 2.8 73.1 + - - +
1021B G 4.7 6.3 + - - -
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Residues in contact with VAL 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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76A ALA* 3.7 29.6 - - + -
81A VAL* 4.3 17.5 - - + -
84A ILE* 3.8 36.6 - - + -
115A PRO* 6.2 1.6 - - + -
119A SER* 2.7 22.8 + - - +
120A ILE 3.3 8.7 - - - +
122A ARG* 1.3 78.9 - - - +
124A LEU* 1.3 57.2 + - - +
126A ASN* 3.1 11.6 + - - +
127A LEU* 2.9 39.1 + - + +
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Residues in contact with LEU 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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84A ILE* 3.7 22.2 - - + +
88A LYS* 3.4 42.2 - - + +
94A ILE 5.7 0.7 - - - +
96A ALA* 5.2 2.9 - - - +
99A ILE* 3.9 21.3 - - + -
120A ILE* 2.8 18.6 + - + +
121A ASN* 3.4 26.5 - - - +
122A ARG 3.2 0.2 - - - -
123A VAL* 1.3 76.5 - - - +
125A ARG* 1.3 63.7 + - + +
127A LEU* 3.3 13.3 + - + +
128A ALA* 3.0 21.7 + - - +
2004C T 5.9 0.4 - - - +
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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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118A SER 5.0 1.0 + - - -
121A ASN* 2.7 32.8 + - - +
122A ARG* 3.1 30.8 + - - +
124A LEU* 1.3 74.0 - - + +
126A ASN* 1.3 66.2 + - - +
128A ALA* 3.0 17.2 + - + +
129A SER* 3.2 15.3 + - - -
2005C G 3.1 61.4 + - - +
2006C T 3.7 38.5 + - - +
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Residues in contact with ASN 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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122A ARG* 2.8 49.5 + - - +
123A VAL* 3.4 9.1 - - - +
125A ARG* 1.3 78.7 - - - +
127A LEU* 1.3 62.4 - - + +
129A SER* 3.4 7.7 + - - -
130A GLU* 3.1 30.4 + - - +
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Residues in contact with LEU 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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81A VAL* 4.1 20.0 - - + +
85A ALA* 4.0 35.9 - - + +
123A VAL* 2.9 36.0 + - + +
124A LEU* 3.7 17.9 - - + +
126A ASN* 1.3 78.0 - - + +
128A ALA* 1.3 61.9 + - - +
130A GLU* 3.2 24.9 - - - +
131A LYS* 3.2 25.3 + - - +
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Residues in contact with ALA 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 LEU 3.0 12.9 + - - +
125A ARG* 3.0 14.2 + - + +
127A LEU* 1.3 78.5 - - - +
129A SER* 1.3 61.2 + - - +
131A LYS* 3.5 16.2 + - - +
132A GLN* 3.5 18.4 + - - +
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Residues in contact with SER 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 3.2 7.7 + - - -
126A ASN* 3.4 12.0 + - - -
128A ALA* 1.3 77.7 - - - +
130A GLU* 1.3 60.5 + - - +
132A GLN* 2.7 39.3 + - - +
133A GLN* 3.0 22.1 + - - +
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Residues in contact with GLU 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 ASN* 3.1 25.1 + - - +
127A LEU* 3.2 30.5 - - - +
128A ALA 3.3 0.2 - - - -
129A SER* 1.3 76.9 + - - +
131A LYS* 1.3 58.2 + - + +
133A GLN* 3.1 33.4 - - + +
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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