Contacts of the helix formed by residues 104 - 120 (chain A) in PDB entry 2XLR
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 PRO 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU 3.4 9.0 - - - +
76A TRP* 3.5 31.9 - - + +
102A TYR 3.7 2.9 - - - +
103A PRO* 1.3 92.5 - - + +
105A ARG* 1.3 67.3 + - - +
106A GLU 3.3 1.8 - - - +
107A VAL* 3.0 19.3 + - + +
108A LEU* 3.2 8.5 + - - +
443A ASP* 3.7 28.9 - - + +
448A TYR* 3.4 40.6 - - + -
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Residues in contact with ARG 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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52A TRP* 2.9 43.4 + - + +
54A TYR* 3.3 40.9 - - - +
71A MET* 3.6 35.4 - - - -
72A TYR 5.0 5.4 + - - +
73A ARG* 6.1 3.0 - - - +
75A LEU* 3.0 26.4 + - + +
76A TRP* 4.4 0.4 - - - +
104A PRO* 1.3 71.5 - - - +
106A GLU* 1.3 92.5 + - - +
108A LEU* 3.1 3.0 + - - +
109A TRP* 2.9 37.1 + - - +
443A ASP* 5.5 4.4 + - - -
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Residues in contact with GLU 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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104A PRO* 3.2 2.2 + - - +
105A ARG* 1.3 103.1 + - - +
107A VAL* 1.3 57.6 + - - +
109A TRP* 3.4 11.8 + - + +
110A ASP* 3.0 27.5 + - - +
443A ASP* 4.1 7.5 + - - +
444A SER* 3.5 11.8 - - - -
445A LEU* 3.3 36.1 + - + +
446A GLU* 3.2 18.4 - - - +
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Residues in contact with VAL 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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91A PHE* 6.1 0.2 - - + -
95A PHE* 3.6 29.7 - - + -
99A ILE* 4.5 6.1 - - + -
103A PRO* 3.6 20.6 - - + -
104A PRO* 3.0 16.7 + - + +
106A GLU* 1.3 75.3 - - - +
108A LEU* 1.3 66.8 + - + +
110A ASP* 3.2 5.5 + - - +
111A TYR* 3.2 15.9 + - - +
445A LEU* 3.9 34.8 - - + +
448A TYR* 3.7 29.8 - - + -
449A LEU* 5.0 3.1 - - + -
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Residues in contact with LEU 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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52A TRP* 3.7 35.4 - - + -
77A SER* 3.8 27.1 - - - +
81A LYS* 4.7 2.2 - - + -
84A LEU* 4.4 20.4 - - + -
91A PHE* 4.2 25.8 - - + -
103A PRO* 3.8 31.4 - - + +
104A PRO 3.2 3.1 + - - +
105A ARG 3.1 6.7 + - - +
107A VAL* 1.3 76.0 - - + +
109A TRP* 1.3 65.2 + - - +
111A TYR* 3.2 7.5 + - + +
112A ILE* 2.8 32.7 + - + +
327A PHE* 5.5 2.0 - - + -
500A FAD 5.1 0.2 - - - +
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Residues in contact with TRP 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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47A ASP* 4.0 14.1 - - - -
48A TRP 3.4 15.9 - - - -
49A GLY* 3.6 18.6 - - - -
52A TRP* 3.5 37.3 - - + +
53A ASN* 4.1 18.4 - - + -
105A ARG* 2.9 33.4 + - - +
106A GLU* 3.4 12.1 - - + +
108A LEU* 1.3 78.2 - - - +
110A ASP* 1.3 64.0 + - - +
112A ILE* 3.2 12.9 + - + +
113A LYS* 2.9 69.8 + - + +
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Residues in contact with ASP 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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94A HIS* 2.8 30.9 + - - +
95A PHE* 4.3 6.7 - - + -
106A GLU 3.0 10.8 + - - +
107A VAL 3.4 9.4 - - - +
109A TRP* 1.3 80.8 - - - +
111A TYR* 1.3 57.3 + - - +
113A LYS* 3.2 15.4 + - - +
114A GLY 2.8 26.3 + - - -
445A LEU* 4.1 20.0 - - + +
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Residues in contact with TYR 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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84A LEU* 4.6 9.6 - - + -
85A GLU* 3.7 5.4 - - - +
86A PHE* 2.8 47.2 + + - -
89A TYR* 2.7 35.1 + + - -
90A THR 3.6 22.0 - - - -
91A PHE* 3.7 42.4 - + + -
94A HIS* 3.7 27.3 + + + -
95A PHE* 3.9 9.6 - + + -
107A VAL 3.2 8.8 + - - +
108A LEU* 3.4 14.4 - - + +
109A TRP 3.2 0.2 - - - -
110A ASP* 1.3 79.4 - - - +
112A ILE* 1.3 73.2 + - + +
114A GLY* 3.2 9.0 + - - -
115A ARG 3.6 7.6 + - - -
327A PHE* 5.4 0.4 - + - -
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Residues in contact with ILE 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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17A PRO* 4.3 24.5 - - + -
20A MET* 4.2 17.8 - - + +
49A GLY* 4.5 3.6 - - - +
52A TRP* 4.4 12.6 - - + -
86A PHE* 4.1 20.4 - - + -
108A LEU* 2.8 28.6 + - + +
109A TRP* 3.2 24.7 + - + +
111A TYR* 1.3 84.6 - - + +
113A LYS* 1.3 66.1 + - - +
114A GLY 3.5 0.2 + - - -
115A ARG* 3.6 10.4 + - - +
116A VAL* 3.4 14.0 + - - +
327A PHE* 4.2 25.1 - - + -
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Residues in contact with LYS 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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20A MET* 4.3 4.5 - - + -
47A ASP* 4.7 3.6 + - - +
48A TRP* 3.2 34.3 - - + +
109A TRP* 2.9 82.6 + - + +
110A ASP* 3.6 13.0 + - - +
112A ILE* 1.3 75.5 - - - +
114A GLY* 1.3 61.8 + - - +
116A VAL* 3.1 8.1 - - - +
117A GLU* 2.8 46.5 + - - +
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Residues in contact with GLY 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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89A TYR* 3.7 19.9 + - - -
94A HIS* 4.0 8.1 - - - -
110A ASP 2.8 16.0 + - - -
111A TYR 3.2 3.2 + - - -
113A LYS* 1.3 76.0 - - - +
115A ARG* 1.3 61.4 + - - +
117A GLU* 3.4 13.0 + - - +
118A LYS* 3.0 26.3 + - - +
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Residues in contact with ARG 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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17A PRO 5.5 0.6 + - - -
20A MET* 4.7 3.0 + - - +
21A ALA* 4.0 13.1 - - - +
24A ARG* 3.4 43.9 + - - +
86A PHE* 3.4 31.4 - - + -
88A ASP* 3.1 26.4 + - - -
89A TYR* 3.6 52.4 - - + -
111A TYR 3.6 0.2 + - - -
112A ILE 3.6 9.0 + - - +
113A LYS 3.3 0.8 - - - -
114A GLY* 1.3 74.9 - - - +
116A VAL* 1.3 62.1 + - - +
118A LYS* 3.5 4.5 + - + +
119A ALA* 3.1 24.4 + - - +
331A ASP* 3.0 39.8 + - - -
335A TRP* 4.7 2.0 - - - -
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Residues in contact with VAL 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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20A MET* 3.2 60.1 - - + +
24A ARG* 4.9 8.1 - - + +
48A TRP* 3.9 20.1 - - + -
112A ILE 3.4 8.1 - - - +
113A LYS* 3.1 17.9 - - - +
115A ARG* 1.3 77.0 - - + +
117A GLU* 1.3 65.2 + - - +
119A ALA* 3.3 4.7 + - - +
120A GLY* 3.2 16.1 + - - -
121A VAL* 3.5 30.8 + - + +
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Residues in contact with GLU 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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48A TRP* 4.0 21.1 + - + -
113A LYS* 2.8 41.3 + - - +
114A GLY* 3.7 12.0 + - - +
116A VAL* 1.3 72.2 - - - +
118A LYS* 1.3 63.4 + - - +
120A GLY* 3.2 14.1 + - - -
122A ARG* 6.4 0.2 - - - -
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Residues in contact with LYS 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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24A ARG* 5.6 7.4 - - - +
88A ASP 5.0 6.1 + - - -
89A TYR* 4.1 23.3 - - + -
93A GLU* 3.2 21.6 + - - +
114A GLY 3.0 15.1 + - - +
115A ARG 3.7 4.5 - - - +
117A GLU* 1.3 79.5 - - - +
119A ALA* 1.3 60.9 + - - +
120A GLY* 3.3 0.7 + - - -
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Residues in contact with ALA 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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24A ARG* 3.2 33.0 - - - +
27A GLN* 3.4 37.8 + - + +
115A ARG 3.1 10.4 + - - +
116A VAL* 3.6 10.3 - - - +
117A GLU 3.2 1.0 - - - -
118A LYS* 1.3 76.1 - - - +
120A GLY* 1.3 61.4 + - - +
121A VAL* 3.6 13.2 + - + -
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Residues in contact with GLY 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 VAL 3.2 1.4 + - - -
117A GLU* 3.2 16.9 + - - -
118A LYS 3.2 1.4 + - - -
119A ALA* 1.3 79.1 - - - +
121A VAL* 1.3 60.7 + - - +
122A ARG* 3.4 4.6 + - - -
123A LYS* 3.8 24.1 + - - +
124A TYR* 4.6 0.5 - - - -
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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