Contacts of the helix formed by residues 104 - 120 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D LEU 3.4 12.6 - - - +
76D TRP* 3.8 26.9 - - + +
102D TYR 3.8 2.9 - - - +
103D PRO* 1.3 92.5 - - + +
105D ARG* 1.3 66.8 + - - +
106D GLU 3.2 2.0 - - - +
107D VAL* 2.9 18.2 + - + +
108D LEU* 3.2 8.4 + - - +
442D ASP 5.7 0.2 - - - +
443D ASP* 3.5 29.8 - - + +
448D TYR* 3.4 40.8 - - + -
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Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D TRP* 3.0 42.6 + - + +
54D TYR* 3.4 40.8 - - - +
71D MET* 3.7 33.9 - - - -
72D TYR 5.0 5.6 + - - +
73D ARG* 6.1 3.0 - - - +
75D LEU* 2.9 27.5 + - + +
76D TRP* 4.3 0.8 - - - +
103D PRO 3.9 0.6 + - - -
104D PRO* 1.3 72.5 - - - +
106D GLU* 1.3 89.6 + - - +
107D VAL 3.1 0.3 + - - -
108D LEU* 3.3 3.0 + - - +
109D TRP* 2.9 40.4 + - - +
443D ASP* 5.6 4.0 + - - -
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Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PRO* 3.2 2.2 - - - +
105D ARG* 1.3 103.3 + - - +
107D VAL* 1.3 58.5 + - - +
109D TRP* 3.4 10.1 + - + +
110D ASP* 3.0 27.7 + - - +
443D ASP* 4.2 8.2 + - - +
444D SER* 3.5 11.1 - - - -
445D LEU* 3.4 36.8 + - + +
446D GLU* 3.3 17.2 - - - +
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PHE* 3.5 29.4 - - + -
99D ILE* 4.4 7.0 - - + -
103D PRO* 3.5 21.8 - - + -
104D PRO* 2.9 16.6 + - + +
106D GLU* 1.3 76.5 - - - +
108D LEU* 1.3 66.3 + - + +
110D ASP* 3.2 5.5 + - - +
111D TYR 3.1 15.8 + - - -
445D LEU* 3.9 33.7 - - + +
448D TYR* 3.6 29.4 - - + -
449D LEU* 5.0 3.1 - - + -
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D TRP* 3.6 34.8 - - + -
77D SER* 4.1 26.9 - - - +
81D LYS* 4.7 2.0 - - + -
84D LEU* 4.3 21.3 - - + -
91D PHE* 4.2 25.6 - - + -
103D PRO* 3.9 31.6 - - + +
104D PRO 3.2 3.1 + - - +
105D ARG 3.9 5.8 - - - +
107D VAL* 1.3 79.0 - - + +
109D TRP* 1.3 63.6 + - - +
111D TYR* 2.9 8.5 + - + +
112D ILE* 2.9 30.6 + - + +
327D PHE* 5.4 2.0 - - + -
500D FAD 5.0 0.2 - - - +
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Residues in contact with TRP 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASP* 3.9 13.9 - - + -
48D TRP 3.4 17.0 - - - -
49D GLY* 3.7 18.4 - - - -
52D TRP* 3.5 35.5 - - + +
53D ASN* 4.2 19.1 - - + -
105D ARG* 2.9 35.9 + - - +
106D GLU* 3.5 12.6 - - + +
108D LEU* 1.3 76.6 - - - +
110D ASP* 1.3 64.3 + - - +
112D ILE* 3.3 12.7 + - + -
113D LYS* 3.0 71.7 + - + +
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D HIS* 2.7 32.0 + - - +
95D PHE* 4.1 7.3 - - + -
106D GLU 3.0 11.2 + - - +
107D VAL 3.4 9.0 - - - +
108D LEU 3.2 0.2 - - - -
109D TRP* 1.3 81.1 - - - +
111D TYR* 1.3 56.4 + - - +
113D LYS* 3.3 14.9 + - - +
114D GLY 3.0 25.1 + - - -
445D LEU* 4.0 19.9 - - + +
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Residues in contact with TYR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 4.5 9.4 - - + -
85D GLU* 3.7 6.4 - - - +
86D PHE* 2.8 45.6 + + - -
89D TYR* 2.8 45.8 + + - -
90D THR 3.7 20.6 - - - -
91D PHE* 3.5 46.0 - + + -
94D HIS* 3.7 24.6 + - + -
95D PHE* 4.0 10.1 - + + -
107D VAL 3.1 8.8 + - - +
108D LEU* 2.9 16.5 + - + +
110D ASP* 1.3 78.8 - - - +
112D ILE* 1.3 69.9 + - + +
114D GLY 3.3 8.5 + - - -
115D ARG 3.7 0.7 + - - -
327D PHE* 5.6 0.2 - + - -
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PRO* 4.4 14.8 - - + -
20D MET* 4.1 21.7 - - + +
49D GLY* 4.6 2.5 - - - -
52D TRP* 4.4 19.7 - - + -
86D PHE* 4.1 23.1 - - + -
108D LEU* 2.9 23.5 + - + +
109D TRP* 3.8 24.2 - - + +
111D TYR* 1.3 83.4 - - + +
113D LYS* 1.3 63.3 + - - +
115D ARG* 3.5 11.3 + - - +
116D VAL* 3.4 13.5 + - - +
327D PHE* 4.3 22.7 - - + -
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D MET* 4.4 4.7 - - + -
47D ASP* 4.6 4.5 + - - +
48D TRP* 3.5 30.5 - - + +
109D TRP* 3.0 82.8 + - + +
110D ASP* 3.7 12.2 + - - +
112D ILE* 1.3 76.6 - - - +
114D GLY* 1.3 59.6 + - - +
116D VAL* 3.2 8.7 - - - +
117D GLU* 2.8 50.6 + - - +
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Residues in contact with GLY 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D TYR* 3.7 20.0 + - - -
94D HIS* 4.0 7.0 - - - -
110D ASP 3.0 14.7 + - - -
111D TYR 3.3 4.0 + - - -
112D ILE 3.3 0.6 - - - -
113D LYS* 1.3 76.1 - - - +
115D ARG* 1.3 61.9 + - - +
117D GLU* 3.8 11.5 + - - +
118D LYS* 3.0 25.5 + - - +
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Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PRO 5.5 0.4 + - - -
20D MET* 4.7 3.0 + - - +
21D ALA* 4.0 13.5 - - - +
24D ARG* 3.0 46.4 + - - +
86D PHE* 3.4 32.5 - - + -
88D ASP* 3.1 31.8 + - - -
89D TYR* 3.6 39.5 - - + -
111D TYR 3.7 4.0 + - - -
112D ILE 3.5 10.1 + - - +
113D LYS 3.2 1.0 - - - -
114D GLY* 1.3 76.7 - - - +
116D VAL* 1.3 64.8 + - - +
118D LYS* 3.4 4.9 + - + +
119D ALA* 3.1 21.4 + - - +
331D ASP* 3.0 40.4 + - - -
335D TRP* 4.8 1.4 - - - -
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D MET* 3.2 61.0 - - + +
24D ARG* 4.9 8.3 - - + -
48D TRP* 3.9 19.2 - - + -
112D ILE 3.4 8.3 - - - +
113D LYS* 3.2 17.7 - - - +
115D ARG* 1.3 76.5 - - + +
117D GLU* 1.3 64.9 + - - +
119D ALA* 3.3 4.7 + - - +
120D GLY 3.1 16.8 + - - -
121D VAL* 3.6 30.6 + - + +
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D TRP* 4.0 19.7 + - + -
113D LYS* 2.8 43.4 + - - +
114D GLY* 3.8 11.8 + - - +
116D VAL* 1.3 77.8 - - - +
118D LYS* 1.3 61.7 + - - +
120D GLY* 3.2 14.0 + - - -
122D ARG* 6.4 0.2 - - - -
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ARG* 6.1 3.0 - - - +
88D ASP 5.3 4.6 + - - -
89D TYR* 4.2 22.4 - - + -
93D GLU* 3.1 22.3 + - - +
114D GLY 3.0 17.3 + - - +
115D ARG* 3.7 4.7 - - + +
117D GLU* 1.3 77.1 - - - +
119D ALA* 1.3 61.1 + - - +
120D GLY* 3.3 0.9 + - - -
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ARG* 3.5 31.2 - - - +
27D GLN* 3.5 33.7 + - - +
115D ARG 3.1 14.3 + - - +
116D VAL* 3.7 9.0 - - - +
117D GLU 3.2 0.4 - - - -
118D LYS* 1.3 77.2 - - - +
120D GLY* 1.3 63.0 + - - +
121D VAL* 4.1 13.5 - - + -
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Residues in contact with GLY 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL 3.1 5.6 + - - -
117D GLU 3.2 9.5 + - - -
118D LYS 3.2 4.8 - - - -
119D ALA* 1.3 78.8 - - - +
121D VAL* 1.3 62.5 + - - +
122D ARG* 3.4 4.0 + - - -
123D LYS* 3.9 24.9 + - - +
124D TYR* 4.7 0.7 - - - -
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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