Contacts of the helix formed by residues 111 - 123 (chain A) in PDB entry 2XAR
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 SER 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ILE* 4.3 7.5 - - - +
5A LEU 3.3 19.9 + - - -
6A GLU* 3.7 21.8 + - - -
110A VAL* 1.3 75.8 - - - +
112A LYS* 1.3 64.0 + - - +
113A GLU* 3.6 14.2 + - - +
114A PHE* 3.1 20.6 + - - +
115A LEU* 3.2 22.5 + - - +
140A HIS 5.5 0.2 - - - -
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A VAL 4.1 0.4 + - - -
111A SER* 1.3 73.2 - - - +
113A GLU* 1.3 74.6 + - - +
115A LEU* 3.3 6.1 + - - +
116A GLU* 2.9 62.6 + - - +
138A THR* 3.3 31.4 - - - +
139A SER* 5.9 0.4 - - - -
140A HIS 5.5 1.0 + - - -
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Residues in contact with GLU 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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6A GLU* 5.2 2.3 - - - +
7A GLU* 4.3 21.0 - - + +
111A SER* 3.2 14.5 + - - +
112A LYS* 1.3 95.6 + - - +
114A PHE* 1.3 59.9 + - - +
116A GLU* 3.8 11.3 - - - +
117A CYS* 2.9 32.1 + - - +
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Residues in contact with PHE 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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5A LEU* 3.3 40.4 - - + +
6A GLU 3.3 21.1 - - - +
7A GLU* 4.2 8.8 - - - +
9A ASP* 4.0 6.5 - - + -
10A ALA* 3.8 26.9 - - + -
13A TRP* 4.1 16.8 - + - -
39A ILE* 4.1 17.0 - - + -
41A ILE* 4.8 2.0 - - + -
110A VAL* 4.0 31.6 - - + -
111A SER* 3.1 13.4 + - - +
113A GLU* 1.3 77.4 - - - +
115A LEU* 1.3 62.4 + - + +
117A CYS* 3.2 4.0 + - - +
118A VAL* 2.8 51.4 + - + +
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Residues in contact with LEU 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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41A ILE* 4.1 33.7 - - + -
110A VAL* 3.9 22.2 - - + -
111A SER 3.2 12.4 + - - +
112A LYS* 3.7 6.5 - - - +
114A PHE* 1.3 90.2 - - + +
116A GLU* 1.3 57.8 + - - +
118A VAL* 3.1 5.2 + - - +
119A ASP* 2.9 30.5 + - - +
136A VAL* 3.7 9.6 - - + +
137A ASP 3.6 19.1 - - - +
138A THR* 3.8 19.1 - - + +
140A HIS* 3.4 27.4 - - + +
142A SER 5.4 1.6 - - - +
143A ALA* 5.5 0.9 - - + -
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Residues in contact with GLU 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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112A LYS* 2.9 50.9 + - - +
113A GLU* 3.9 13.2 - - - +
115A LEU* 1.3 75.3 - - - +
117A CYS* 1.3 61.4 + - - +
119A ASP* 3.8 5.4 - - - +
120A LYS* 3.3 23.9 + - - +
138A THR* 3.7 24.4 + - + -
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Residues in contact with CYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU* 3.5 35.4 - - + -
10A ALA* 4.0 18.2 - - + -
113A GLU 2.9 19.9 + - - +
114A PHE 3.4 4.0 - - - +
116A GLU* 1.3 74.6 - - - +
118A VAL* 1.3 59.7 + - - +
120A LYS* 3.5 3.9 + - - +
121A LYS* 2.9 31.4 + - - +
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Residues in contact with VAL 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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10A ALA* 4.1 16.4 - - + +
13A TRP* 5.3 4.9 - - + -
23A LEU* 4.5 7.9 - - + -
25A LEU* 3.7 32.3 - - + -
41A ILE* 4.2 11.2 - - + -
114A PHE* 2.8 49.3 + - + +
115A LEU* 3.5 7.0 - - - +
117A CYS* 1.3 73.0 - - - +
119A ASP* 1.3 67.3 + - - +
121A LYS* 3.2 9.2 + - + +
122A VAL* 3.0 27.2 + - + +
136A VAL* 5.1 2.0 - - + -
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Residues in contact with ASP 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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23A LEU* 5.3 0.3 - - - +
115A LEU 2.9 10.2 + - - +
116A GLU* 3.8 8.1 - - - +
118A VAL* 1.3 77.5 - - - +
120A LYS* 1.3 52.6 + - - +
122A VAL* 3.5 9.0 + - - +
123A THR* 2.6 39.1 + - - -
126A ARG* 3.7 13.6 + - - -
135A ASN* 3.4 25.4 + - - +
136A VAL* 3.3 44.7 + - + +
138A THR* 5.6 0.4 - - + -
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Residues in contact with LYS 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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116A GLU 3.3 14.5 + - - +
117A CYS* 4.0 3.6 - - - +
118A VAL 3.3 0.4 - - - -
119A ASP* 1.3 76.9 - - - +
121A LYS* 1.3 66.3 + - - +
122A VAL 3.3 0.3 + - - -
123A THR* 3.5 19.1 + - - +
124A LYS* 4.8 1.4 + - - +
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Residues in contact with LYS 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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10A ALA* 3.9 13.7 - - + +
11A SER* 3.4 35.5 + - - +
13A TRP 3.3 23.7 + - - +
14A ILE* 4.8 6.9 - - - +
15A TYR 5.7 0.2 - - - +
117A CYS* 2.9 20.4 + - - +
118A VAL* 3.2 8.7 + - + +
120A LYS* 1.3 78.4 - - - +
122A VAL* 1.3 67.3 + - + +
124A LYS* 4.7 5.0 + - - +
125A GLN* 3.6 16.8 + - - +
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Residues in contact with VAL 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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13A TRP 5.3 0.4 - - - +
14A ILE 5.2 0.2 - - - -
15A TYR* 4.3 21.5 - - + +
23A LEU* 4.2 21.5 - - + -
25A LEU* 3.8 25.8 - - + -
118A VAL* 3.0 22.0 + - + +
119A ASP* 3.5 11.0 - - - +
121A LYS* 1.3 89.8 - - + +
123A THR* 1.3 67.6 + - - +
124A LYS 3.0 3.6 - - - -
125A GLN* 2.8 26.1 + - - +
126A ARG* 3.4 21.1 + - - +
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Residues in contact with THR 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 ASP* 2.6 30.4 + - - -
120A LYS* 3.5 15.2 + - - +
122A VAL* 1.3 77.0 - - - +
124A LYS* 1.3 62.5 + - - +
126A ARG* 3.4 27.9 + - - +
131A VAL* 4.3 24.8 - - + +
182B LYS* 5.1 5.6 - - - +
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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