Contacts of the helix formed by residues 108 - 122 (chain A) in PDB entry 2XWU
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.9 1.1 - - - +
12A GLU* 3.6 20.2 - - - +
68A TYR* 5.5 0.7 - - - -
106A ALA 3.7 11.9 - - - +
107A ILE* 1.3 73.2 - - - +
109A ILE* 1.3 63.6 + - - +
110A LYS* 3.5 9.9 + - - +
111A GLN* 2.8 38.3 + - - +
112A ILE* 3.1 30.3 + - - +
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Residues in contact with ILE 109 (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 LEU* 4.8 1.1 - - + -
12A GLU* 3.5 37.0 + - + +
16A TRP* 4.0 17.3 - - + -
26A ALA* 4.4 7.2 - - + -
41A TRP* 3.8 35.0 - - + -
62A MET* 4.0 20.2 - - + -
64A PHE* 4.4 16.8 - - + -
68A TYR* 5.0 2.2 - - - +
108A THR* 1.3 73.5 - - - +
110A LYS* 1.3 65.0 + - - +
112A ILE* 4.0 9.0 - - + +
113A LEU* 3.3 39.8 + - + +
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Residues in contact with LYS 110 (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 TRP* 3.8 18.8 - - + -
19A ASP* 2.7 49.6 + - - +
21A PRO* 4.0 29.3 - - + +
108A THR* 3.2 10.3 + - - +
109A ILE* 1.3 78.8 - - - +
111A GLN* 1.3 67.7 + - - +
113A LEU* 4.1 1.0 - - - +
114A LEU* 3.0 31.2 + - + +
261B GLU* 3.9 12.5 + - - -
264B VAL* 4.2 2.2 - - - +
265B ASN* 3.6 22.1 + - - +
310B ARG* 3.9 8.5 - - - +
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Residues in contact with GLN 111 (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 ILE* 4.5 4.1 - - + +
104A ARG* 4.9 11.7 + - - +
106A ALA 3.9 2.6 - - - +
107A ILE* 3.0 24.8 - - + +
108A THR* 2.8 41.3 + - - +
109A ILE 3.3 0.4 - - - -
110A LYS* 1.3 81.8 - - + +
112A ILE* 1.3 54.9 + - - +
114A LEU* 3.3 6.5 + - - +
115A GLY* 2.7 33.6 + - - -
231B GLN* 3.7 25.7 - - - +
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Residues in contact with ILE 112 (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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62A MET* 4.6 10.5 - - - -
64A PHE* 5.4 1.8 - - + -
68A TYR* 5.8 1.3 - - + +
73A PRO* 3.8 26.0 - - + -
75A CYS* 3.9 16.8 - - - -
96A ILE* 4.3 11.5 - - + +
97A LEU* 3.7 26.2 - - + -
103A TRP* 3.9 17.5 - - + -
107A ILE* 3.7 12.8 - - + +
108A THR 3.1 19.0 + - - +
109A ILE* 4.0 13.9 - - + +
111A GLN* 1.3 74.3 - - - +
113A LEU* 1.3 59.5 + - + +
115A GLY* 3.0 4.2 + - - -
116A ILE* 2.8 37.8 + - + +
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Residues in contact with LEU 113 (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 TRP* 3.4 37.5 - - + -
24A PHE* 3.9 18.2 - - + -
25A VAL 4.7 1.6 - - - +
26A ALA* 4.2 8.1 - - + -
43A CYS* 4.3 9.9 - - + -
44A ALA 5.9 0.4 - - - +
45A ILE* 3.7 25.2 - - + +
60A LEU* 4.0 14.4 - - + -
62A MET* 3.6 24.2 - - + -
109A ILE* 3.3 20.5 + - + +
110A LYS 4.1 2.2 - - - +
112A ILE* 1.3 72.7 - - - +
114A LEU* 1.3 61.2 + - - +
116A ILE* 3.2 8.0 + - + +
117A GLN* 2.9 28.6 + - - +
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Residues in contact with LEU 114 (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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21A PRO* 3.9 25.1 - - + -
24A PHE* 3.5 29.4 - - + -
110A LYS* 3.0 30.3 + - + +
111A GLN* 3.8 5.4 - - - +
113A LEU* 1.3 74.8 - - - +
115A GLY* 1.3 63.2 + - - +
117A GLN* 3.2 14.5 + - - +
118A GLU* 3.0 24.1 + - - +
261B GLU* 4.3 19.5 - - - +
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Residues in contact with GLY 115 (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 LEU* 3.8 15.6 - - - +
96A ILE* 4.6 7.6 - - - -
111A GLN 2.7 15.7 + - - -
112A ILE 3.0 4.5 + - - -
114A LEU* 1.3 78.7 - - - +
116A ILE* 1.3 60.0 + - - +
118A GLU* 3.5 13.0 + - - +
119A LEU* 3.1 21.8 + - - +
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Residues in contact with ILE 116 (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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45A ILE* 3.5 19.1 - - + -
60A LEU* 4.4 11.0 - - + -
75A CYS* 3.9 36.3 - - + -
77A PHE* 3.6 27.8 - - + -
92A VAL* 4.4 13.0 - - + -
94A LEU* 3.8 18.6 - - + -
97A LEU* 4.3 3.1 - - + -
112A ILE* 2.8 24.1 + - + +
113A LEU* 3.2 8.9 + - + +
115A GLY* 1.3 74.6 - - - +
117A GLN* 1.3 66.6 + - - +
119A LEU* 3.1 7.1 + - + +
120A LEU* 3.1 21.9 + - + +
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Residues in contact with GLN 117 (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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24A PHE* 3.3 29.2 - - + -
45A ILE* 3.5 19.5 - - + +
46A PRO* 3.1 32.0 + - - +
47A GLY 4.7 0.2 + - - -
48A LYS* 3.7 47.7 + - + +
113A LEU 2.9 13.0 + - - +
114A LEU* 3.2 14.7 + - - +
116A ILE* 1.3 76.8 - - - +
118A GLU* 1.3 63.1 + - - +
120A LEU* 3.4 20.5 + - + +
121A ASN* 3.8 3.8 + - - +
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Residues in contact with GLU 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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48A LYS* 5.0 17.9 - - - +
114A LEU 3.0 14.7 + - - +
115A GLY* 3.7 11.9 - - - +
117A GLN* 1.3 78.8 + - - +
119A LEU* 1.3 57.6 + - - +
120A LEU 3.2 0.5 + - - -
121A ASN* 3.3 6.0 + - - +
122A GLU* 3.0 40.2 + - + +
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Residues in contact with LEU 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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83A HIS* 2.8 24.4 + - + -
85A ASN* 2.8 33.2 - - + +
86A VAL* 6.1 0.9 - - + -
92A VAL* 3.8 20.9 - - + -
93A CYS 3.7 16.2 - - - +
94A LEU* 3.6 29.6 - - + -
115A GLY 3.1 11.4 + - - +
116A ILE* 3.1 11.2 + - + +
118A GLU* 1.3 78.3 - - - +
120A LEU* 1.3 62.1 + - + +
122A GLU 3.2 26.5 - - - +
124A ASN* 3.7 9.2 - - + +
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Residues in contact with LEU 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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45A ILE* 4.6 10.5 - - + -
47A GLY* 5.0 6.1 - - - -
48A LYS 6.0 0.7 - - - +
53A TRP* 3.1 55.7 + - + -
58A PHE* 3.8 32.1 - - + -
77A PHE* 4.0 26.9 - - + -
81A LEU* 4.3 5.4 - - + -
83A HIS* 3.4 15.9 + - + +
86A VAL* 5.6 0.4 - - + -
116A ILE* 3.1 16.8 + - + +
117A GLN* 3.5 16.6 - - - +
118A GLU 3.1 0.4 - - - -
119A LEU* 1.3 81.4 - - + +
121A ASN* 1.3 62.6 + - - +
123A PRO* 4.2 4.3 - - - +
144A TYR* 4.3 0.7 + - - -
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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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48A LYS* 5.0 13.1 - - + +
51A THR* 3.1 41.4 - - + +
52A PRO* 4.3 8.5 - - - +
53A TRP* 3.8 12.4 + - + +
117A GLN 3.8 5.2 + - - +
118A GLU* 3.3 6.9 + - - +
120A LEU* 1.3 80.8 - - - +
122A GLU* 1.3 72.9 + - + +
123A PRO* 3.5 7.3 - - - +
137A TYR* 5.0 1.7 + - - -
144A TYR* 6.0 1.2 - - - -
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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
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118A GLU* 3.0 26.2 + - + +
119A LEU* 3.2 23.5 - - - +
121A ASN* 1.3 95.7 + - + +
123A PRO* 1.3 67.6 - - - +
124A ASN* 3.5 0.5 + - - +
137A TYR* 4.9 2.2 - - - +
118B ILE* 6.0 2.0 - - - +
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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