Contacts of the helix formed by residues 116 - 130 (chain A) in PDB entry 1ATT
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 THR 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.7 18.4 - - + -
24A TYR 3.5 4.0 - - - +
25A ARG* 4.5 8.2 - - - +
104A MET* 5.4 0.2 - - - -
114A GLU* 3.1 19.5 + - - +
115A LYS* 1.3 87.9 - - + +
117A SER* 1.3 66.6 + - - +
118A ASP* 3.0 19.3 + - - +
119A GLN* 2.9 26.5 + - - +
120A ILE* 4.0 7.1 - - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A CYS 4.2 1.2 + - - -
23A ILE* 3.1 12.8 - - - -
24A TYR* 2.7 40.6 + - - -
25A ARG* 5.2 1.4 - - - +
92A LYS* 3.7 17.0 + - - -
100A LEU* 4.0 10.1 - - - +
104A MET* 3.8 36.2 - - - +
116A THR* 1.3 71.8 - - - +
118A ASP* 1.3 62.5 + - - +
119A GLN 3.1 0.9 + - - -
120A ILE* 3.3 12.2 + - - +
121A HIS* 3.9 1.6 + - - -
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Residues in contact with ASP 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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18A VAL* 3.2 36.2 - - + +
19A ASN* 4.9 1.7 - - - +
20A PRO* 4.0 27.4 - - + -
23A ILE* 3.6 22.2 - - + +
116A THR* 2.9 28.4 + - - +
117A SER* 1.3 81.3 + - - +
119A GLN* 1.3 77.4 + - - +
120A ILE 3.4 0.3 + - - -
121A HIS* 3.5 11.4 + - - +
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Residues in contact with GLN 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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18A VAL* 5.6 2.4 - - - +
114A GLU* 3.4 32.5 + - + +
116A THR* 2.9 18.4 + - - +
118A ASP* 1.3 88.5 - - - +
120A ILE* 1.4 54.2 + - - +
122A PHE* 2.7 41.2 + - - +
123A PHE* 3.2 47.8 + - + -
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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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52A LEU* 5.2 1.1 - - + -
89A ALA* 5.5 2.0 - - + -
92A LYS* 4.6 8.1 - - - +
104A MET* 3.9 22.2 - - + -
109A PHE* 4.0 46.0 - - + +
112A ILE* 3.7 37.2 - - + +
114A GLU* 4.8 5.8 - - + +
116A THR 4.0 14.6 - - - +
117A SER* 3.3 9.0 + - - +
119A GLN* 1.4 79.1 - - + +
121A HIS* 1.3 64.7 + - + +
123A PHE* 3.0 10.7 + - - +
124A PHE* 2.8 26.7 + - + +
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Residues in contact with HIS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.1 13.5 - - + +
20A PRO* 5.1 4.7 - - + +
89A ALA* 2.9 21.5 + - + +
92A LYS* 3.0 42.2 + - - -
93A LEU* 3.3 33.5 + - + +
117A SER 3.9 2.4 + - - -
118A ASP* 3.7 17.2 + - - +
119A GLN 3.0 0.8 + - - -
120A ILE* 1.3 77.6 - - + +
122A PHE* 1.3 62.7 + - - +
124A PHE* 3.1 10.6 + - - +
125A ALA 3.2 1.6 + - - -
166A VAL* 3.0 28.1 - - + +
167A TYR* 2.8 33.0 - + - -
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Residues in contact with PHE 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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8A VAL* 6.3 0.2 - - + -
9A CYS* 4.4 5.2 - - - -
14A ARG* 4.8 5.2 - - + -
16A ILE* 3.9 34.1 - - + -
18A VAL* 4.8 12.4 - - + +
46A ASN* 3.6 24.9 - - + -
118A ASP 4.2 1.4 + - - +
119A GLN* 2.7 30.3 + - - +
121A HIS* 1.3 71.6 - - - +
123A PHE* 1.3 91.9 + + - +
125A ALA* 2.9 18.3 + - + +
126A LYS* 3.0 51.0 + - + +
166A VAL* 4.8 3.8 - - - -
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Residues in contact with PHE 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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46A ASN* 4.4 10.8 - - + -
48A ARG* 3.5 32.8 - - + -
49A VAL* 3.9 9.3 - - + +
52A LEU* 3.5 21.7 - - + +
112A ILE* 3.7 22.7 - - + -
114A GLU* 3.4 26.5 - - + -
119A GLN* 3.4 44.4 - - + -
120A ILE* 3.0 8.9 + - - +
122A PHE* 1.3 107.0 - + - +
124A PHE* 1.3 59.1 + - - +
126A LYS* 3.3 7.4 + - - +
127A LEU* 3.0 19.6 + - - +
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Residues in contact with PHE 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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52A LEU* 3.8 20.6 - - + +
56A ASN* 3.8 32.5 - - - -
82A LEU* 4.0 11.2 - - + -
85A SER* 4.2 11.2 - - - -
86A THR* 3.3 37.7 - - + -
89A ALA* 4.3 11.4 - - + -
109A PHE* 4.3 7.0 - + - -
120A ILE* 2.8 16.8 + - + +
121A HIS 3.1 8.3 + - - +
122A PHE 3.0 0.2 + - - -
123A PHE* 1.3 71.7 - - - +
125A ALA* 1.3 57.7 + - - +
126A LYS 3.2 0.2 + - - -
127A LEU* 3.3 6.8 + - + -
128A ASN* 2.8 61.2 + - - -
167A TYR* 3.8 24.5 - + + +
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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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7A ASP* 6.0 0.2 - - - +
8A VAL* 4.2 15.7 - - + -
9A CYS* 3.2 9.2 - - + +
16A ILE* 6.4 0.2 - - + -
121A HIS 3.2 3.8 + - - -
122A PHE* 2.9 12.0 + - + +
124A PHE* 1.3 76.1 - - - +
126A LYS* 1.3 61.8 + - - +
128A ASN* 3.7 11.5 - - - +
129A CYS* 3.1 26.5 + - - +
166A VAL* 3.3 37.4 - - + +
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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
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9A CYS* 2.6 33.4 + - + +
10A THR* 3.7 5.5 - - + +
14A ARG* 2.8 30.1 - - - +
46A ASN* 3.9 21.8 - - - +
47A ARG* 6.0 0.7 - - - +
49A VAL* 3.7 15.3 - - + -
122A PHE* 3.0 33.2 + - + +
123A PHE* 3.5 11.7 - - - +
125A ALA* 1.3 80.2 - - - +
127A LEU* 1.3 61.9 + - - +
129A CYS* 3.8 2.4 - - + +
130A ARG* 3.2 47.9 + - - +
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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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49A VAL* 3.6 41.1 - - + +
52A LEU* 4.1 10.3 - - + -
53A SER* 3.9 23.3 - - - +
56A ASN* 5.0 3.4 - - - +
82A LEU* 4.8 10.3 - - + -
123A PHE 3.0 14.9 + - - +
124A PHE* 4.0 11.2 - - + +
126A LYS* 1.3 75.5 - - - +
128A ASN* 1.3 61.4 + - - +
130A ARG* 3.3 6.6 + - - -
131A LEU* 3.2 43.1 + - + +
418A LEU* 3.9 14.1 - - + -
420A THR* 4.0 14.6 - - + -
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Residues in contact with ASN 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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82A LEU* 5.3 0.9 - - - +
86A THR* 4.4 7.4 + - - +
124A PHE* 2.8 60.9 + - - +
125A ALA* 3.7 8.3 - - - +
126A LYS 3.4 0.2 - - - -
127A LEU* 1.3 75.0 - - - +
129A CYS* 1.3 63.2 + - - +
131A LEU* 2.9 11.3 + - - -
132A TYR* 3.0 46.9 + - + +
143A SER* 6.0 0.2 - - - -
145A ASN* 5.6 2.7 + - - +
166A VAL 4.1 10.1 + - - +
167A TYR* 4.3 9.9 - - - +
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Residues in contact with CYS 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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6A GLU* 3.5 32.4 - - - +
9A CYS* 2.0 57.9 - - + -
10A THR* 3.5 14.4 - - - +
125A ALA 3.1 7.9 + - - +
126A LYS* 3.8 3.1 - - + +
128A ASN* 1.3 75.3 - - - +
130A ARG* 1.3 57.9 + - - +
131A LEU 2.9 5.9 + - - -
132A TYR* 4.5 0.6 - - - -
133A ARG* 3.6 23.7 + - - +
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Residues in contact with ARG 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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10A THR* 3.3 30.0 + - - +
47A ARG* 4.0 21.6 - - - +
49A VAL* 5.6 6.7 - - + -
126A LYS* 3.2 36.4 + - - +
127A LEU* 3.4 9.2 - - - +
128A ASN 3.2 0.4 - - - -
129A CYS* 1.3 77.5 - - - +
131A LEU* 1.3 54.4 + - - +
133A ARG* 5.1 4.9 - - - -
415A GLU* 4.9 0.9 - - - +
418A LEU* 3.1 42.7 - - + +
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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