Contacts of the helix formed by residues 98 - 118 (chain A) in PDB entry 1MRA
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 GLY 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 1.3 86.4 + - - +
99A LEU* 1.3 63.8 + - - -
101A ARG* 2.9 14.1 + - - +
102A MET* 2.9 20.1 + - - +
250A LEU* 3.7 19.9 - - - +
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Residues in contact with LEU 99 (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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58A ALA* 4.9 16.8 - - + -
61A SER* 3.9 25.4 - - - +
62A LEU* 3.2 51.3 - - + +
65A LEU* 3.6 10.5 - - + +
97A THR 3.5 0.4 + - - -
98A GLY* 1.3 72.4 - - - -
100A ILE* 1.3 58.4 + - + +
102A MET* 3.3 15.5 + - + +
103A ALA* 2.8 26.7 + - - +
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Residues in contact with ILE 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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65A LEU* 3.8 24.0 - - + -
69A MET* 4.8 3.2 - - - +
91A PHE* 3.5 59.2 - - + -
94A ALA* 4.2 17.5 - - + +
95A GLY 3.8 17.0 - - - +
96A TYR* 4.4 7.9 - - + -
97A THR 3.4 7.4 + - - +
98A GLY 3.0 0.8 + - - -
99A LEU* 1.3 78.3 - - + +
101A ARG* 1.3 57.3 + - - +
103A ALA* 3.3 4.0 + - - +
104A ALA* 2.9 26.7 + - - +
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Residues in contact with ARG 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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84A GLU* 5.3 1.8 + - - -
96A TYR* 3.0 58.0 + - - -
97A THR* 3.3 20.0 + - - +
98A GLY 2.9 9.5 + - - +
100A ILE* 1.3 79.6 - - - +
102A MET* 1.3 59.3 + - - +
104A ALA* 3.1 6.8 + - - +
105A ALA* 2.8 29.2 + - - +
250A LEU* 4.3 9.4 + - + -
251A GLY* 3.2 22.0 - - - +
252A PRO* 3.3 10.7 - - - +
253A GLU* 2.4 43.8 + - - -
272A MET 5.2 0.4 - - - -
273A LYS* 4.6 14.6 - - - +
274A ILE 4.7 0.6 + - - -
275A GLY* 4.7 13.2 - - - -
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Residues in contact with MET 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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51A LEU* 3.5 9.7 - - - +
52A PHE 3.7 12.1 - - - +
53A ALA* 5.2 1.8 - - - -
54A TYR* 4.2 15.3 - - + -
62A LEU* 4.0 17.7 - - + -
98A GLY* 2.9 21.0 + - - +
99A LEU* 3.3 20.8 + - + +
101A ARG* 1.3 74.9 - - - +
103A ALA* 1.3 64.3 + - - +
105A ALA* 3.0 14.1 + - - +
106A GLY 3.0 10.9 + - - -
250A LEU* 4.2 15.5 - - + -
272A MET* 3.3 41.3 - - + +
273A LYS* 4.5 13.5 - - + -
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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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51A LEU* 4.0 9.6 - - - -
62A LEU* 3.9 10.0 - - + +
65A LEU* 3.9 6.3 - - + -
66A LEU* 3.8 26.1 - - + +
69A MET* 3.8 16.8 - - - -
99A LEU 2.8 17.2 + - - +
100A ILE 3.6 4.7 - - - +
102A MET* 1.3 75.7 - - - +
104A ALA* 1.3 62.5 + - - +
106A GLY* 3.0 10.7 + - - -
107A ILE* 3.2 17.4 + - - +
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Residues in contact with ALA 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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69A MET* 4.8 6.6 - - + +
84A GLU* 6.5 0.2 - - + -
87A LEU* 4.2 24.0 - - + +
91A PHE* 6.0 0.7 - - + -
96A TYR* 4.1 25.1 - - + +
100A ILE* 2.9 15.4 + - + +
101A ARG* 3.1 12.8 + - - +
103A ALA* 1.3 75.8 - - - +
105A ALA* 1.3 62.6 + - - +
107A ILE* 3.2 7.3 + - - +
108A ASP* 3.1 22.6 + - - +
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Residues in contact with ALA 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 ARG 2.8 12.0 + - - +
102A MET 3.0 9.6 + - - +
104A ALA* 1.3 74.3 - - - +
106A GLY* 1.3 65.9 + - - +
108A ASP* 3.3 3.1 + - - +
109A MET* 3.1 30.5 + - - +
272A MET* 2.8 37.7 - - - +
275A GLY* 3.9 8.3 - - - -
276A GLY* 3.6 17.4 - - - +
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Residues in contact with GLY 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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37A ILE* 4.0 14.3 - - - +
49A SER* 2.8 23.4 + - - -
51A LEU* 3.6 24.8 - - - +
102A MET 3.0 10.1 + - - -
103A ALA 3.0 4.4 + - - -
105A ALA* 1.3 78.5 - - - +
107A ILE* 1.3 60.2 + - - +
109A MET* 3.9 3.8 - - - -
110A ALA* 3.3 10.9 + - - +
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Residues in contact with ILE 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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9A LEU* 4.1 19.7 - - + -
37A ILE* 5.2 2.2 - - + -
39A LEU* 4.5 8.1 - - + +
66A LEU* 3.9 13.5 - - + -
69A MET* 4.2 22.7 - - + -
73A ILE* 3.2 42.6 - - + -
83A LEU* 4.9 17.7 - - + -
87A LEU* 5.1 7.0 - - + -
103A ALA 3.2 11.5 + - - +
104A ALA* 3.5 8.7 - - - +
105A ALA 3.2 0.6 - - - -
106A GLY* 1.3 74.1 - - - +
108A ASP* 1.3 60.7 + - - +
110A ALA* 3.2 7.6 + - - +
111A ALA* 2.9 28.2 + - + +
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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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80A PRO* 3.7 12.5 - - - +
83A LEU* 6.5 0.4 - - - -
84A GLU* 4.6 7.0 - - + +
104A ALA 3.1 13.4 + - - +
105A ALA* 3.6 8.1 - - - +
107A ILE* 1.3 77.3 - - - +
109A MET* 1.3 56.7 + - - +
111A ALA* 3.4 6.8 + - - +
112A TRP* 3.0 37.0 + - - -
275A GLY 3.9 9.2 - - - +
277A VAL 2.6 33.3 + - - -
278A THR* 2.3 36.9 + - - -
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Residues in contact with MET 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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48A HIS 4.0 2.8 - - - +
49A SER* 3.8 12.8 - - - -
50A TYR 4.0 9.2 - - - +
51A LEU* 3.8 27.8 - - + -
105A ALA 3.1 21.1 + - - +
106A GLY* 3.9 2.7 - - - -
107A ILE 3.2 0.2 - - - -
108A ASP* 1.3 76.1 - - - +
110A ALA* 1.3 63.2 + - - +
112A TRP* 3.5 4.8 + - - +
113A ASP* 3.0 21.8 + - - +
271A ALA* 4.2 17.7 - - - -
272A MET* 4.2 15.0 - - + +
276A GLY* 3.6 22.2 - - - -
277A VAL* 4.1 1.8 - - - +
299A PHE* 4.6 6.7 - - + -
302A ILE* 4.1 37.5 - - + +
345A VAL* 5.0 0.5 - - - +
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Residues in contact with ALA 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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37A ILE* 4.0 10.5 - - + -
39A LEU* 3.9 25.4 - - + -
47A GLY* 3.8 5.1 - - - -
48A HIS 3.5 19.1 - - - +
49A SER* 3.8 9.5 - - - +
106A GLY 3.3 10.1 + - - +
107A ILE* 3.2 8.8 + - - +
109A MET* 1.3 74.0 - - - +
111A ALA* 1.3 55.8 + - - +
113A ASP* 2.9 5.4 + - - +
114A ALA* 2.8 34.5 + - - +
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Residues in contact with ALA 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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39A LEU* 3.8 17.1 - - + +
78A LEU* 3.6 17.8 - - + +
80A PRO* 4.1 22.6 - - + +
83A LEU* 4.7 10.8 - - + -
107A ILE* 2.9 18.2 + - + +
108A ASP* 3.4 9.9 - - - +
110A ALA* 1.3 76.9 - - - +
112A TRP* 1.3 56.3 + - - +
114A ALA 3.4 0.7 + - - +
115A LEU* 2.9 29.1 + - - +
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Residues in contact with TRP 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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80A PRO* 3.4 20.2 - - + +
81A VAL* 4.4 20.9 - - + -
108A ASP* 3.0 27.7 + - - +
109A MET 3.9 2.0 - - - +
111A ALA* 1.3 73.2 - - - +
113A ASP* 1.3 60.6 + - - +
115A LEU* 3.2 20.0 + - + +
116A GLY* 2.9 25.6 + - - -
123A LEU* 4.1 17.9 - - + +
126A LEU* 4.0 30.2 - - + +
127A LEU* 3.9 18.8 - - + -
277A VAL* 3.1 46.2 - - + +
278A THR* 2.9 20.1 + - - -
281A ILE* 4.4 9.9 - - + -
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Residues in contact with ASP 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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47A GLY* 3.3 1.6 - - - -
48A HIS* 2.7 32.1 + - - +
109A MET 3.0 13.5 + - - +
110A ALA 2.9 9.3 + - - +
112A TRP* 1.3 76.5 - - - +
114A ALA* 1.3 57.7 + - - +
116A GLY* 3.1 3.3 + - - -
117A LYS* 2.6 60.5 + - - +
123A LEU* 5.8 0.4 - - - -
344A GLY* 3.5 10.9 - - - -
345A VAL* 2.8 41.5 + - + +
346A GLY 4.2 2.8 + - - -
347A ILE* 4.8 3.5 + - - -
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Residues in contact with ALA 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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39A LEU* 4.6 2.0 - - + +
41A THR* 4.1 23.1 - - + -
45A VAL* 4.1 2.9 - - + +
46A VAL 4.5 1.1 - - - -
47A GLY* 3.7 20.6 - - - +
78A LEU* 4.2 6.7 - - + -
110A ALA 2.8 18.4 + - - +
111A ALA* 3.7 5.4 - - - +
113A ASP* 1.3 70.2 - - - +
115A LEU* 1.3 61.5 + - - +
117A LYS* 3.3 10.5 + - - +
118A VAL* 2.9 34.8 + - - +
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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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78A LEU* 3.9 26.7 - - + +
80A PRO* 4.1 22.4 - - + -
111A ALA 2.9 18.4 + - - +
112A TRP* 3.2 29.3 + - + +
114A ALA* 1.3 76.9 - - - +
116A GLY* 1.3 60.5 + - - +
118A VAL* 3.7 6.6 + - + +
119A HIS* 3.3 49.2 + - + +
126A LEU* 4.0 11.2 - - + +
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Residues in contact with GLY 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 TRP 2.9 13.8 + - - -
113A ASP 3.5 4.9 - - - -
114A ALA 3.1 0.6 - - - -
115A LEU* 1.3 77.9 - - - +
117A LYS* 1.3 58.5 + - - +
119A HIS* 3.3 2.6 + - - +
120A GLU 3.1 5.2 + - - -
121A THR* 2.9 43.4 + - - -
123A LEU* 5.4 1.1 - - - -
126A LEU* 3.9 13.2 - - - +
344A GLY* 3.8 7.9 - - - -
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Residues in contact with LYS 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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45A VAL* 3.9 26.1 - - + +
46A VAL 2.8 28.8 + - - +
48A HIS* 3.6 20.2 + - - -
113A ASP* 2.6 45.5 + - - +
114A ALA* 3.3 5.4 + - - +
116A GLY* 1.3 71.7 - - - +
118A VAL* 1.3 68.2 + - - +
119A HIS 3.0 1.8 - - - -
120A GLU* 2.9 18.7 + - - +
343A PRO* 4.0 28.0 - - + +
347A ILE 4.5 3.6 + - - -
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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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4A VAL* 4.8 14.8 - - + -
43A ALA* 4.3 13.2 - - + -
45A VAL* 3.6 23.1 - - + -
78A LEU* 4.2 15.9 - - + -
114A ALA 2.9 26.6 + - - +
115A LEU* 3.7 10.3 - - + +
117A LYS* 1.3 77.2 - - - +
119A HIS* 1.3 83.7 + - + +
120A GLU* 3.5 4.3 + - - +
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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