Contacts of the helix formed by residues 105 - 123 (chain A) in PDB entry 1XGG
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 ASN 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS* 2.8 13.6 + - + +
104A PHE* 1.3 74.4 - - - +
106A VAL* 1.3 58.7 + - - +
107A GLY* 3.0 8.5 + - - -
108A ARG* 3.0 56.0 + - + +
109A ALA* 3.0 27.9 + - - +
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Residues in contact with VAL 106 (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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68A MET* 4.5 33.7 - - + +
71A ALA* 5.1 8.7 - - + +
72A GLN* 3.5 26.2 - - - +
75A SER* 4.1 20.6 - - - +
104A PHE* 5.6 4.5 - - + -
105A ASN* 1.3 70.4 + - - +
107A GLY* 1.3 64.6 + - - +
109A ALA* 4.5 0.7 - - - -
110A TYR* 2.9 31.6 + - + +
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Residues in contact with GLY 107 (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 ASN* 3.0 7.6 + - - -
106A VAL* 1.3 79.1 - - - +
108A ARG* 1.3 57.4 + - - +
110A TYR* 3.2 2.9 + - - +
111A GLU* 2.9 44.4 + - - +
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Residues in contact with ARG 108 (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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102A ARG* 3.3 41.5 + - + +
103A LYS* 5.3 16.1 - - - +
105A ASN* 3.0 38.5 + - + +
107A GLY* 1.3 72.6 - - - +
109A ALA* 1.3 64.3 + - - +
111A GLU* 3.1 15.5 + - - +
112A LEU 3.0 18.9 + - - -
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Residues in contact with ALA 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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72A GLN* 3.5 24.8 + - + +
98A PHE* 5.1 8.1 - - + +
99A ILE* 5.1 10.5 - - + -
102A ARG* 4.5 10.8 - - - +
103A LYS 4.5 10.3 - - - +
104A PHE* 6.2 1.8 - - + -
105A ASN 3.0 15.2 + - - +
106A VAL* 4.5 0.7 - - - -
108A ARG* 1.3 76.4 - - - +
110A TYR* 1.3 57.1 + - - +
112A LEU* 3.5 3.6 + - - +
113A LEU* 3.1 23.6 + - - +
230A PHE* 3.6 12.2 - - + -
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Residues in contact with TYR 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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72A GLN* 3.8 12.1 - - - +
75A SER* 3.1 32.1 + - - +
76A GLY* 3.8 9.0 - - - -
78A GLU* 4.8 10.0 + - - +
79A LEU* 4.1 22.3 - - + +
106A VAL* 2.9 23.3 + - + +
107A GLY* 3.8 3.6 - - - +
109A ALA* 1.3 75.1 - - - +
111A GLU* 1.3 64.0 + - + +
113A LEU* 3.2 21.3 + - + +
114A ARG* 3.0 49.3 + - - +
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Residues in contact with GLU 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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102A ARG* 3.9 12.3 + - - +
107A GLY* 2.9 23.8 + - - +
108A ARG* 3.1 25.4 + - - +
110A TYR* 1.3 81.0 - - + +
112A LEU* 1.3 57.9 + - - +
114A ARG* 3.5 5.8 + - - +
115A GLY* 3.0 23.7 + - - -
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Residues in contact with LEU 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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98A PHE 4.5 2.0 - - - +
101A ALA* 3.7 25.1 - - + -
102A ARG* 3.7 38.1 - - + +
108A ARG 3.0 15.8 + - - +
109A ALA* 3.7 2.9 - - - +
111A GLU* 1.3 73.7 - - - +
113A LEU* 1.3 63.1 + - - +
115A GLY* 3.5 3.6 + - - +
116A TYR* 3.2 18.4 + - - +
226A LEU 4.9 4.0 - - - +
227A GLN* 4.4 23.3 - - + +
230A PHE* 3.4 51.7 - - + -
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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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72A GLN* 3.9 13.5 - - + +
76A GLY* 3.9 21.3 - - - +
79A LEU* 4.4 11.0 - - + -
83A VAL* 5.9 0.9 - - + -
94A PHE* 5.2 5.4 - - + -
95A PHE* 4.7 22.7 - - + -
98A PHE* 5.2 2.0 - - + -
109A ALA 3.1 13.0 + - - +
110A TYR* 3.2 31.4 - - + +
112A LEU* 1.3 75.8 - - - +
114A ARG* 1.3 63.7 + - - +
116A TYR* 3.3 3.6 + - - +
117A VAL* 3.1 42.5 + - + +
230A PHE* 3.0 23.8 - - + -
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Residues in contact with ARG 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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79A LEU* 4.0 22.9 - - + +
110A TYR* 3.0 38.2 + - + +
111A GLU* 4.0 6.3 - - - +
112A LEU 3.5 0.2 - - - -
113A LEU* 1.3 72.9 - - - +
115A GLY* 1.3 66.4 + - - +
117A VAL 3.2 0.7 + - - -
118A ASN* 3.0 51.5 + - - +
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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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111A GLU 3.0 17.0 + - - -
112A LEU* 3.8 5.4 - - - -
113A LEU 3.3 0.4 - - - -
114A ARG* 1.3 78.8 - - - +
116A TYR* 1.3 60.3 + - - +
118A ASN* 3.4 13.2 + - - +
119A PHE* 3.5 10.9 + - - +
227A GLN* 5.2 3.1 - - - -
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Residues in contact with TYR 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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83A VAL* 4.7 1.3 - - + -
94A PHE* 4.2 25.4 - + - -
112A LEU 3.2 6.4 + - - +
113A LEU 3.9 0.2 - - - +
115A GLY* 1.3 74.4 - - - +
117A VAL* 1.3 68.5 + - + +
119A PHE* 3.1 15.3 + + + +
120A ARG* 3.1 55.1 + - + +
125A GLU* 6.4 0.7 - - + -
227A GLN 3.7 15.7 + - - +
228A ASP* 3.5 25.2 - - + +
229A SER* 3.3 44.1 - - - -
230A PHE* 3.8 30.1 - + + -
233A ARG* 5.6 0.2 + - - -
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Residues in contact with VAL 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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79A LEU* 3.7 39.7 - - + +
82A ALA* 4.6 3.6 - - + -
83A VAL* 3.7 31.2 - - + -
94A PHE* 6.2 0.2 - - + -
113A LEU* 3.1 35.7 + - + +
114A ARG 3.2 3.1 + - - +
116A TYR* 1.3 80.1 - - + +
118A ASN* 1.3 63.6 + - - +
119A PHE 3.3 0.9 + - - -
120A ARG* 3.3 15.5 + - + +
121A LEU* 3.4 29.9 + - + +
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Residues in contact with ASN 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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79A LEU* 5.4 2.8 - - - +
114A ARG* 3.0 46.4 + - - +
115A GLY* 3.7 6.7 + - - +
117A VAL* 1.3 79.5 - - - +
119A PHE* 1.3 62.3 + - - +
121A LEU* 3.5 9.0 + - - +
122A GLN* 3.3 28.0 + - - +
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Residues in contact with PHE 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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115A GLY 3.5 7.9 + - - +
116A TYR* 3.1 11.9 + + - +
118A ASN* 1.3 78.1 - - - +
120A ARG* 1.3 64.9 + - + +
122A GLN* 3.3 4.2 + - - -
123A TYR* 2.8 70.6 + + + +
125A GLU* 4.9 17.9 - - + -
224A ASP* 3.8 25.1 - - - -
228A ASP* 3.5 33.2 - - - +
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Residues in contact with ARG 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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82A ALA 5.0 1.9 + - - +
83A VAL* 4.2 27.1 + - + +
86A ARG* 5.2 5.7 - - - +
87A VAL* 6.0 4.2 - - - +
116A TYR* 3.1 60.6 + - + +
117A VAL* 3.3 8.3 + - + +
119A PHE* 1.3 80.1 - - + +
121A LEU* 1.3 62.3 + - + +
122A GLN 3.4 0.2 - - - -
123A TYR 3.2 15.6 - - - +
124A PRO* 5.1 0.7 - - - +
125A GLU* 4.1 37.8 + - + +
126A LEU* 3.3 55.4 + - + +
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Residues in contact with LEU 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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79A LEU* 5.7 2.5 - - + -
82A ALA* 4.5 20.9 - - + +
117A VAL* 3.4 34.4 + - + +
118A ASN* 3.5 7.6 + - - +
119A PHE 3.3 0.4 - - - -
120A ARG* 1.3 78.5 - - + +
122A GLN* 1.3 60.6 + - - +
126A LEU* 3.8 22.0 - - + -
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Residues in contact with GLN 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 ASN* 3.3 17.2 + - - +
119A PHE* 3.3 2.8 + - - +
121A LEU* 1.3 81.5 - - - +
123A TYR* 1.3 101.7 + - + +
124A PRO* 4.3 2.4 - - - +
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Residues in contact with TYR 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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119A PHE* 2.8 60.4 + + + +
120A ARG* 3.2 12.9 - - - +
121A LEU 5.3 0.2 - - - -
122A GLN* 1.3 117.9 + - + +
124A PRO* 1.3 71.8 - - + +
125A GLU* 3.0 10.8 + - - +
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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