Contacts of the helix formed by residues 99 - 111 (chain A) in PDB entry 1XRE
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLU 4.3 5.6 + - - +
98A PRO* 1.3 73.2 - - - +
100A GLY* 1.3 71.6 + - - +
102A VAL* 3.7 11.8 - - - +
103A ALA* 3.7 11.8 + - - -
192A TRP* 3.6 27.7 - - - +
193A ASP* 3.4 26.4 + - - +
196A ASN* 4.1 6.2 + - - +
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Residues in contact with GLY 100 (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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99A ASN* 1.3 80.7 - - - +
101A ASP* 1.3 66.6 + - - +
103A ALA* 3.2 17.1 + - - +
104A LYS* 3.9 9.7 + - - +
196A ASN* 4.2 7.6 - - - -
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Residues in contact with ASP 101 (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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100A GLY* 1.3 72.2 - - - -
102A VAL* 1.3 62.6 + - - +
104A LYS* 3.2 39.2 + - + +
105A VAL* 3.5 7.3 + - - +
196A ASN* 3.2 14.5 + - - +
199A TYR* 4.8 9.0 - - + -
200A LEU* 3.8 26.4 - - + +
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Residues in contact with VAL 102 (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 PRO* 4.9 4.5 - - + -
99A ASN 3.7 9.0 - - - +
101A ASP* 1.3 72.6 - - - +
103A ALA* 1.3 62.4 + - - +
104A LYS 3.1 1.8 - - - -
105A VAL* 3.1 21.1 - - + +
106A ILE* 2.9 46.7 + - + +
135A LEU* 5.6 0.9 - - + -
142A LEU* 4.5 4.5 - - + -
161A LEU* 4.8 4.9 - - + -
192A TRP* 4.9 4.0 - - + +
195A VAL* 4.5 15.0 - - + -
196A ASN* 3.0 37.2 - - + +
199A TYR* 3.8 27.4 - - + -
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Residues in contact with ALA 103 (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 PRO* 3.6 41.1 - - + +
99A ASN* 3.7 3.1 + - - -
100A GLY 3.2 13.1 + - - +
102A VAL* 1.3 80.7 - - - +
104A LYS* 1.3 58.7 + - + +
106A ILE* 3.4 4.2 + - - +
107A ASP* 3.1 35.1 + - - +
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Residues in contact with LYS 104 (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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100A GLY 4.0 9.6 - - - +
101A ASP* 3.3 30.6 + - + +
102A VAL 3.1 0.2 - - - -
103A ALA* 1.3 76.9 - - + +
105A VAL* 1.3 59.9 + - - +
107A ASP* 3.3 9.2 + - - +
108A TYR* 3.0 25.5 + - - +
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Residues in contact with VAL 105 (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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101A ASP 3.5 2.4 + - - +
102A VAL* 3.1 35.2 - - + +
104A LYS* 1.3 75.8 - - - +
106A ILE* 1.3 64.7 + - - +
108A TYR* 3.2 6.1 + - + +
109A TYR* 3.1 47.4 + - + +
140A GLU 4.4 3.8 - - - +
142A LEU* 3.5 28.3 - - + +
199A TYR* 3.8 29.4 - - + +
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Residues in contact with ILE 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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98A PRO* 3.8 28.0 - - + -
102A VAL* 2.9 30.7 + - + +
103A ALA 3.6 4.5 - - - +
104A LYS 3.2 0.2 - - - -
105A VAL* 1.3 75.5 - - - +
107A ASP* 1.3 66.6 + - - +
109A TYR 3.2 1.0 + - - -
110A PHE* 2.9 35.7 + - + +
112A THR 4.6 0.7 - - - +
113A PHE* 4.3 21.1 - - + +
116A LEU* 3.9 35.2 - - + -
135A LEU* 4.7 6.5 - - + -
142A LEU* 3.9 18.6 - - + -
192A TRP* 4.1 11.4 - - + -
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Residues in contact with ASP 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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103A ALA* 3.1 16.8 + - - +
104A LYS* 3.7 9.4 - - - +
106A ILE* 1.3 77.1 - - - +
108A TYR* 1.3 59.6 + - - +
111A ASN* 2.8 45.2 + - - +
112A THR* 4.1 1.0 - - - -
113A PHE* 3.9 21.0 + - - +
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Residues in contact with TYR 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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104A LYS 3.0 14.6 + - - +
105A VAL* 3.4 13.9 - - + +
106A ILE 3.2 0.2 - - - -
107A ASP* 1.3 79.4 - - - +
109A TYR* 1.3 98.4 + + + +
111A ASN* 4.5 1.2 + - - -
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Residues in contact with TYR 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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105A VAL* 3.1 41.2 + - + +
108A TYR* 1.3 107.1 - + - +
110A PHE* 1.3 73.9 + - + +
111A ASN 3.7 0.2 - - - -
140A GLU* 3.2 38.5 + - - +
141A GLU* 3.6 29.8 + - + +
142A LEU* 3.7 24.7 - - + +
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Residues in contact with PHE 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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106A ILE* 2.9 23.3 + - + +
109A TYR* 1.3 83.2 - - + +
111A ASN* 1.3 63.7 + - - +
112A THR 2.9 23.4 + - - +
115A ASN* 2.9 28.3 + - - +
116A LEU* 3.8 45.3 - - + +
119A GLN* 3.2 33.2 - - - -
135A LEU* 4.2 4.5 - - + -
142A LEU* 3.9 42.2 - - + -
143A SER* 4.2 3.8 - - - -
144A VAL* 4.2 15.9 - - + -
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Residues in contact with ASN 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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107A ASP* 2.8 36.2 + - - +
108A TYR 4.4 1.2 + - - -
109A TYR 3.7 1.0 - - - -
110A PHE* 1.3 77.5 - - - +
112A THR* 1.3 72.8 + - - +
115A ASN* 5.3 1.1 - - + +
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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