Contacts of the helix formed by residues 100 - 117 (chain A) in PDB entry 5XJY
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLN* 3.8 19.0 + - - -
97A PHE* 3.2 31.3 + - - +
98A ASN 3.1 6.1 + - - +
99A LYS* 1.3 76.2 - - - +
101A ILE* 1.3 59.3 + - - +
102A VAL 4.4 0.9 - - - -
103A ALA* 3.0 22.4 + - - +
104A ARG* 3.4 5.5 + - - +
307A ILE 4.4 1.6 - - - -
308A VAL 2.5 33.3 + - - -
309A CYS* 3.3 5.3 - - - +
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Residues in contact with ILE 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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99A LYS 3.9 8.3 - - - +
100A SER* 1.3 69.3 - - - +
102A VAL* 1.3 64.0 + - - +
104A ARG* 3.4 34.6 + - - +
105A LEU* 3.3 19.1 + - - +
277A SER* 3.4 14.2 + - - +
280A ASP* 4.9 10.1 - - + +
281A MET* 3.8 38.8 - - + +
284A GLU* 4.3 11.4 - - + +
306A ARG* 4.3 8.7 + - + +
307A ILE* 3.2 36.3 + - + +
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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
----------------------------------------------------------
67A LEU* 4.3 14.4 - - + -
71A GLN* 4.3 9.9 - - - +
100A SER 3.1 0.4 - - - -
101A ILE* 1.3 78.7 - - + +
103A ALA* 1.3 61.6 + - - +
105A LEU* 3.2 29.0 + - + +
106A PHE* 3.5 28.4 - - + -
281A MET* 5.3 2.2 - - + -
307A ILE* 3.3 37.2 - - + +
308A VAL* 4.0 13.2 - - + -
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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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67A LEU* 4.1 15.4 - - + +
71A GLN* 4.2 14.5 - - - +
97A PHE* 3.9 18.4 - - + +
98A ASN 5.0 1.6 - - - +
100A SER* 3.0 12.7 + - - +
102A VAL* 1.3 80.3 - - - +
104A ARG* 1.3 52.0 + - + +
105A LEU 3.3 0.2 + - - -
106A PHE* 3.4 3.5 + - - +
107A SER* 2.7 36.5 + - - +
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Residues in contact with ARG 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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98A ASN 4.2 18.5 + - - +
99A LYS* 4.3 14.3 + - - +
100A SER 3.4 7.5 + - - +
101A ILE* 3.4 36.6 + - - +
102A VAL 3.3 0.4 - - - -
103A ALA* 1.3 75.0 - - + +
105A LEU* 1.3 60.2 + - - +
107A SER* 3.4 10.1 - - - +
108A ASP* 2.9 36.8 + - - +
111A ARG* 5.2 2.9 + - - +
275A MET 6.1 0.4 - - - -
277A SER* 3.9 14.2 + - - +
280A ASP* 4.8 11.9 + - - +
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Residues in contact with LEU 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 ILE 3.3 10.7 + - - +
102A VAL* 3.2 21.0 + - + +
103A ALA 3.2 0.2 - - - -
104A ARG* 1.3 77.0 - - - +
106A PHE* 1.3 67.9 + - + +
108A ASP* 3.0 9.8 + - + +
109A ALA* 2.9 21.5 + - - +
277A SER* 3.3 27.3 + - - +
278A TRP* 3.9 32.1 - - + +
281A MET* 4.6 22.9 - - + -
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Residues in contact with PHE 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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67A LEU* 3.8 22.0 - - + -
102A VAL* 3.5 32.1 - - + -
103A ALA 3.4 4.9 + - - +
105A LEU* 1.3 81.8 - - + +
107A SER* 1.3 60.1 + - - +
109A ALA* 3.2 12.1 + - + +
110A ARG* 3.0 27.3 + - - +
409A PHE* 5.0 17.9 - + - -
1577A LEU* 6.2 2.0 - - + -
1580A PHE* 4.0 32.5 - + - -
1581A MET* 3.7 22.2 - - + +
1584A LEU* 4.3 13.5 - - + +
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Residues in contact with SER 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* 2.7 25.0 + - - +
104A ARG* 3.4 12.7 - - - +
106A PHE* 1.3 76.7 - - - +
108A ASP* 1.3 60.7 + - - +
110A ARG* 3.2 11.9 + - - +
111A ARG* 3.0 34.0 + - - +
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Residues in contact with ASP 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 ARG* 2.9 21.1 + - - +
105A LEU* 3.0 9.6 + - + +
107A SER* 1.3 73.5 - - - +
109A ALA* 1.3 60.5 + - - +
111A ARG* 2.4 36.5 + - - +
112A LEU* 2.8 38.4 + - + +
275A MET* 2.8 43.3 - - + +
277A SER* 3.2 14.7 - - - -
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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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105A LEU 2.9 7.7 + - - +
106A PHE* 3.2 24.2 + - + +
108A ASP* 1.3 75.6 - - - +
110A ARG* 1.3 57.8 + - - +
112A LEU* 4.2 4.7 - - - +
113A LEU* 3.0 43.1 + - + +
1577A LEU* 5.7 5.2 - - + -
1581A MET* 4.1 16.2 - - + -
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE 3.0 13.1 + - - +
107A SER* 3.5 12.0 - - - +
108A ASP 3.2 0.2 - - - -
109A ALA* 1.3 78.3 - - - +
111A ARG* 1.3 55.8 + - - +
113A LEU* 4.8 1.1 - - - -
114A LEU* 2.9 51.0 + - + +
1544A ALA* 3.4 25.8 - - - +
1545A LEU* 3.8 33.1 + - + +
1551A VAL* 4.8 12.6 - - + +
1581A MET* 3.5 31.9 + - - -
1584A LEU* 3.4 42.8 + - - +
1585A ASP* 4.7 4.9 - - - +
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Residues in contact with ARG 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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104A ARG* 5.2 2.6 + - - +
107A SER* 3.0 21.2 + - - +
108A ASP* 2.4 36.1 + - - +
110A ARG* 1.3 77.1 - - - +
112A LEU* 1.3 58.8 + - - +
114A LEU* 4.3 0.2 - - - +
115A TYR* 2.9 31.2 + - - +
271A GLU* 4.6 3.2 - - - +
274A SER* 4.1 10.1 + - - -
275A MET* 3.6 40.8 + - + +
1545A LEU* 3.7 21.8 - - + -
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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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108A ASP* 2.8 21.7 + - + +
109A ALA* 4.2 4.3 - - - +
111A ARG* 1.3 73.5 - - - +
113A LEU* 1.3 63.7 + - + +
115A TYR* 4.0 3.0 - - + +
116A SER* 2.9 30.1 + - - -
268A LEU* 6.4 1.6 - - + -
271A GLU* 4.5 16.6 - - + +
272A LEU* 5.1 14.6 - - + -
275A MET* 4.1 28.3 - - + -
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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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109A ALA* 3.0 24.9 + - + +
110A ARG* 4.2 2.0 - - - +
112A LEU* 1.3 79.4 - - + +
114A LEU* 1.3 64.3 + - + +
116A SER* 3.1 6.7 + - - -
117A GLN* 2.9 27.7 + - - +
1551A VAL* 5.2 4.7 - - + -
1554A ALA* 3.9 12.2 - - + +
1555A ILE* 3.9 30.3 - - + -
1558A MET* 4.8 19.3 - - + +
1574A LEU* 5.8 2.0 - - + -
1577A LEU* 4.0 22.4 - - + -
1581A MET* 4.4 19.1 - - + -
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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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110A ARG* 2.9 32.5 + - + +
111A ARG 3.8 0.4 - - - +
113A LEU* 1.3 83.3 - - + +
115A TYR* 1.3 58.8 + - - +
117A GLN* 4.0 19.3 - - + +
118A LYS* 4.4 6.8 + - - +
1545A LEU* 3.7 34.8 - - + -
1546A PRO* 3.7 24.0 - - + +
1550A GLU* 4.6 19.0 - - + +
1551A VAL* 3.7 40.2 - - + -
1554A ALA* 4.7 2.7 - - + -
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Residues in contact with TYR 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 ARG 2.9 15.6 + - - +
112A LEU* 4.1 2.9 - - + +
114A LEU* 1.3 76.4 - - - +
116A SER* 1.3 54.3 + - - +
117A GLN 3.1 5.2 - - - -
118A LYS* 2.7 49.1 + - + -
119A ASP* 3.3 37.8 + - + -
267A THR* 3.3 34.7 - - - +
268A LEU* 3.6 18.2 - - + -
271A GLU* 3.1 42.0 - - - +
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Residues in contact with SER 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 LEU 2.9 19.5 + - - -
113A LEU* 3.1 7.4 + - - -
115A TYR* 1.3 75.4 - - - +
117A GLN* 1.3 63.1 + - - +
118A LYS 3.2 0.6 + - - -
119A ASP* 4.1 17.9 + - - +
1557A GLN* 5.0 1.6 + - - +
1558A MET* 3.5 32.2 - - - +
1561A HIS* 5.5 4.7 + - - -
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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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113A LEU 2.9 8.5 + - - +
114A LEU* 4.0 11.3 - - + +
116A SER* 1.3 78.4 - - - +
118A LYS* 1.3 91.8 + - - +
119A ASP 3.7 1.1 + - - -
1550A GLU* 3.7 19.8 + - + +
1553A ASP* 4.8 3.4 - - + +
1554A ALA* 3.7 38.6 + - + +
1557A GLN* 2.5 51.0 + - + +
1558A MET 6.0 0.2 - - - +
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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
------------------------------------------------------------
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