Contacts of the helix formed by residues 104 - 115 (chain G) in PDB entry 1XBT
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 ASP 104 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU* 3.3 27.3 - - + +
80G LEU* 3.8 17.9 - - + +
81G LEU* 3.0 26.2 + - - +
82G ARG* 3.0 36.4 + - - +
102G PHE* 3.9 6.1 - - - +
103G PRO* 1.3 78.3 - - - +
105G ILE* 1.3 63.5 + - - -
106G VAL 3.3 2.5 - - - -
107G GLU* 3.4 13.8 + - + -
108G PHE* 3.1 25.2 + - + +
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Residues in contact with ILE 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G LEU* 3.6 23.8 - - + -
96G ILE* 4.0 22.4 - - + -
99G GLY* 3.8 22.4 - - - +
100G GLN* 5.8 0.4 - - - -
102G PHE* 3.3 18.2 + - + +
103G PRO 3.5 1.2 - - - -
104G ASP* 1.3 76.6 + - - +
106G VAL* 1.3 76.1 + - + +
108G PHE* 4.0 0.7 - - - +
109G CYS* 3.1 48.2 + - - +
121G VAL* 4.3 5.8 - - + -
135G ALA* 4.5 13.2 - - + +
136G ILE* 4.5 15.5 - - + +
139G LEU* 4.3 13.7 - - + -
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Residues in contact with VAL 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ARG* 3.3 30.3 - - - +
104G ASP 3.3 1.0 - - - -
105G ILE* 1.3 84.1 - - + +
107G GLU* 1.3 71.5 + - - +
109G CYS* 4.0 1.2 - - - +
110G GLU* 3.1 24.8 + - - +
135G ALA* 3.8 19.7 - - + +
138G ASN* 3.7 33.9 - - + +
139G LEU* 4.1 10.2 - - + +
142G LEU* 3.7 20.9 - - + -
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Residues in contact with GLU 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ARG* 4.3 23.8 + - + +
104D ASP* 3.6 22.9 - - + +
107D GLU* 3.3 38.8 - - + -
103G PRO 3.6 7.4 - - - +
104G ASP* 3.4 28.9 - - + +
106G VAL* 1.3 86.6 + - - +
108G PHE* 1.3 55.8 + - - +
110G GLU* 4.1 0.5 - - - +
111G ALA* 3.0 31.5 + - - +
135G ALA* 6.1 0.2 - - - +
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Residues in contact with PHE 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ILE* 4.2 13.9 - - + -
81G LEU* 3.5 52.3 - - + -
82G ARG* 4.6 1.1 - - - -
84G VAL 5.0 0.7 - - - -
85G ALA* 4.2 7.6 - - + -
88G ALA* 3.8 24.9 - - + -
94G ILE* 4.2 9.2 - - + -
96G ILE* 3.8 24.5 - - + -
104G ASP* 3.1 20.9 + - + +
105G ILE 4.0 2.0 - - - +
107G GLU* 1.3 75.7 - - - +
109G CYS* 1.3 62.9 + - - +
111G ALA* 3.4 4.1 + - - +
112G MET* 2.9 67.3 + - + +
119G VAL* 4.8 1.6 - - + -
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Residues in contact with CYS 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ILE* 3.7 22.0 - - + +
96G ILE* 3.9 5.4 - - - -
105G ILE* 3.1 36.1 + - - +
108G PHE* 1.3 79.1 - - - +
110G GLU* 1.3 58.4 + - - +
112G MET* 3.9 0.9 - - - +
113G ALA* 2.9 32.9 + - - +
119G VAL* 3.7 19.2 - - + +
121G VAL* 3.7 30.5 - - - -
139G LEU* 3.8 11.4 - - + -
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Residues in contact with GLU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ARG* 3.8 33.7 - - + +
130E ARG* 2.4 38.3 + - - +
186E ARG* 3.2 18.2 + - - -
190E PHE* 3.7 2.4 - - - -
21G ILE* 3.9 4.9 - - - +
106G VAL 3.1 18.7 + - - +
107G GLU 4.1 0.7 - - - +
109G CYS* 1.3 78.5 - - - +
111G ALA* 1.3 56.5 + - - +
113G ALA* 3.9 0.2 - - - -
114G ASN* 2.9 60.7 + - - +
142G LEU* 3.7 20.3 - - + +
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Residues in contact with ALA 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ARG* 6.1 0.4 - - - +
107G GLU 3.0 19.9 + - - +
108G PHE* 3.8 4.0 - - - +
110G GLU* 1.3 78.2 - - - +
112G MET* 1.3 65.0 + - + +
114G ASN* 3.5 6.6 + - - +
115G ALA* 3.1 28.4 + - - +
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Residues in contact with MET 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G ALA* 3.9 22.2 - - + +
88G ALA* 4.1 11.2 - - + -
89G LEU* 3.7 33.2 - - + -
94G ILE* 4.0 9.6 - - + -
108G PHE* 2.9 55.1 + - + +
111G ALA* 1.3 79.3 - - + +
113G ALA* 1.3 64.0 + - - +
115G ALA* 3.3 7.2 + - - -
116G GLY 3.4 0.5 + - - -
117G LYS* 2.9 40.4 + - + +
119G VAL* 3.8 18.4 - - + -
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Residues in contact with ALA 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ARG* 3.6 31.7 - - - +
19G GLY* 3.2 17.7 + - - -
20G GLN 3.7 15.7 - - - +
21G ILE* 3.7 13.2 - - + -
109G CYS 2.9 18.0 + - - +
110G GLU 4.0 0.2 - - - +
112G MET* 1.3 76.1 - - - +
114G ASN* 1.3 58.8 + - - +
116G GLY* 3.1 14.4 + - - -
117G LYS 3.5 10.1 - - - -
119G VAL* 4.1 1.6 - - + +
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Residues in contact with ASN 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ARG* 3.0 26.2 + - - +
187E LEU* 6.0 1.2 - - - +
190E PHE* 3.6 24.8 - - - -
110G GLU* 2.9 47.6 + - - +
111G ALA* 3.9 6.4 - - - +
113G ALA* 1.3 74.3 - - - +
115G ALA* 1.3 56.5 + - - +
116G GLY 3.2 4.3 + - - -
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Residues in contact with ALA 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G LEU* 5.1 9.6 - - + -
111G ALA 3.1 18.0 + - - +
112G MET* 3.7 6.3 - - - +
113G ALA 3.2 0.6 - - - -
114G ASN* 1.3 75.0 - - - +
116G GLY* 1.3 59.3 + - - +
117G LYS* 3.5 22.3 + - + +
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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