Contacts of the helix formed by residues 69 - 89 (chain A) in PDB entry 1XRE
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 ILE 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 3.7 21.5 - - + +
44A LEU* 4.4 2.7 - - + -
47A TYR* 3.5 47.6 - - + +
50A LEU* 3.9 28.0 - - + -
65A LEU* 4.5 4.3 - - + -
66A PRO* 3.0 24.0 + - + +
68A GLU* 1.3 84.4 - - + +
70A VAL* 1.3 65.8 - - - +
71A THR 3.2 3.1 - - - -
72A ALA* 3.2 8.5 + - + +
73A VAL* 2.9 38.9 + - + +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.4 38.6 - - + +
63A GLU* 5.3 0.7 - - - -
65A LEU* 4.4 13.7 - - + +
66A PRO 3.1 10.4 + - - +
67A LYS* 3.5 39.2 + - + +
69A ILE* 1.3 76.3 - - - +
71A THR* 1.3 72.5 + - - +
73A VAL* 3.3 1.0 + - - +
74A ARG* 2.8 35.3 + - + +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS 5.0 1.0 + - - -
69A ILE 3.2 1.0 - - - -
70A VAL* 1.3 86.2 - - - +
72A ALA* 1.3 57.8 + - - +
74A ARG* 3.1 9.8 + - + +
75A ASN* 2.8 52.5 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN 5.3 0.4 - - - +
40A LEU* 5.0 0.5 - - - +
43A ALA* 3.8 24.5 - - + +
68A GLU 5.5 1.8 + - - +
69A ILE* 3.2 13.9 + - + +
71A THR* 1.3 78.6 - - - +
73A VAL* 1.3 59.4 + - - +
75A ASN* 4.8 0.9 - - - -
76A ASN* 2.9 47.2 + - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.4 13.2 - - + -
43A ALA* 4.4 10.8 - - + -
44A LEU* 4.2 22.2 - - + -
58A LEU* 4.0 24.2 - - + -
59A LEU* 4.0 3.5 - - + +
62A LEU* 4.0 7.4 - - + -
65A LEU* 3.6 31.2 - - + -
69A ILE* 2.9 27.2 + - + +
70A VAL 3.8 0.2 - - - +
72A ALA* 1.3 76.3 - - - +
74A ARG* 1.3 61.7 + - - +
77A GLY* 2.8 32.1 + - - +
78A GLY 3.7 0.3 + - - -
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.3 3.4 - - + +
62A LEU* 4.0 31.7 - - + +
70A VAL* 2.8 25.1 + - + +
71A THR* 3.5 9.9 - - - +
73A VAL* 1.3 73.7 - - - +
75A ASN* 1.3 65.5 + - - +
78A GLY* 3.0 26.0 + - - -
150A GLN* 4.1 5.2 - - - +
151A ASP* 2.9 43.0 + - - +
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 4.1 0.7 - - - -
71A THR* 2.8 42.6 + - - +
72A ALA* 4.3 2.2 - - - +
74A ARG* 1.3 87.7 + - - +
76A ASN* 1.3 64.3 + - - +
79A GLY* 2.9 21.3 + - - -
149A ASN* 5.4 1.6 - - - +
150A GLN* 3.5 14.8 + - - +
151A ASP* 4.9 2.9 - - - +
128B PHE* 3.4 56.7 - - + +
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Residues in contact with ASN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.3 43.5 - - - +
39A ASN* 3.3 37.3 + - - +
40A LEU* 3.7 12.3 - - - +
72A ALA* 2.9 42.6 + - - +
75A ASN* 1.3 76.1 - - - +
77A GLY* 1.3 60.1 + - - +
79A GLY* 3.2 0.9 + - - -
80A HIS* 2.9 29.6 + - - +
128B PHE* 5.1 2.0 - - - -
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Residues in contact with GLY 77 (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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40A LEU* 3.8 24.2 - - - +
55A LEU* 3.6 10.3 - - - +
58A LEU* 6.3 0.2 - - - -
59A LEU* 4.0 9.4 - - - -
73A VAL* 2.8 18.7 + - - -
76A ASN* 1.3 71.9 - - - +
78A GLY* 1.3 65.1 + - - +
80A HIS* 3.2 2.9 + - - +
81A TYR* 2.9 24.4 + - - +
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Residues in contact with GLY 78 (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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59A LEU* 3.8 15.2 - - - +
73A VAL 3.7 0.8 + - - -
74A ARG 3.0 18.2 + - - -
77A GLY* 1.3 74.6 - - - +
79A GLY* 1.3 56.6 + - - +
81A TYR 3.2 0.7 + - - -
82A CYS* 2.9 35.3 + - - -
150A GLN* 3.2 26.7 - - - -
152A THR* 4.3 2.2 - - - -
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A HIS* 4.3 0.4 - - - -
36A TYR* 3.8 16.6 - - - -
75A ASN 2.9 16.0 + - - -
76A ASN 3.2 3.8 + - - -
77A GLY 3.2 0.2 - - - -
78A GLY* 1.3 75.0 - - - +
80A HIS* 1.3 63.4 + - - +
83A HIS* 2.9 31.9 + - - +
150A GLN* 3.3 22.6 - - - +
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Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.9 39.0 - + + +
5A GLN 3.3 27.3 + - - -
7A PRO* 4.0 4.0 - - + -
33A HIS* 2.9 31.2 + - - -
36A TYR* 4.0 3.0 - - + +
37A VAL* 3.5 16.1 - - + +
40A LEU* 4.1 10.1 - - + -
55A LEU* 3.9 15.8 - - + +
76A ASN 2.9 16.7 + - - +
77A GLY 3.6 4.0 - - - +
79A GLY* 1.3 76.7 - - - +
81A TYR* 1.3 61.3 + - - +
84A SER* 2.8 45.4 + - - -
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.7 16.5 - - + +
56A GLU* 3.4 26.9 - - + -
59A LEU* 3.6 16.4 - - + -
77A GLY 2.9 16.3 + - - +
78A GLY* 3.7 2.5 - - - +
80A HIS* 1.3 77.8 - - - +
82A CYS* 1.3 68.3 + - - +
84A SER* 3.8 3.3 - - - -
85A LEU* 3.2 31.8 + - + +
134A TRP* 4.2 12.8 - + - -
152A THR* 4.0 19.1 - - + -
154A LEU* 3.8 22.6 - - + +
160A PRO* 3.3 41.6 + - + +
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Residues in contact with CYS 82 (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 GLY 2.9 23.1 + - - +
81A TYR* 1.3 78.8 - - - +
83A HIS* 1.3 57.3 + - - +
85A LEU* 3.5 2.9 + - - +
86A PHE* 3.0 27.3 + - - +
132A TYR* 3.4 40.2 - - + +
134A TRP* 3.7 33.7 - - + -
150A GLN* 3.8 16.4 - - - +
151A ASP 4.2 0.7 - - - -
152A THR* 4.0 8.7 - - - -
163A VAL* 4.0 5.0 - - - +
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Residues in contact with HIS 83 (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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28A HIS* 3.0 22.6 + + - -
32A HIS* 5.0 1.3 - - + +
33A HIS* 3.5 24.5 - + + +
36A TYR* 3.5 29.5 - + - -
79A GLY 2.9 26.7 + - - +
82A CYS* 1.3 76.0 - - - +
84A SER* 1.3 66.9 + - - +
86A PHE* 3.1 9.1 + + - +
87A TRP* 3.0 41.7 + + - +
132A TYR* 3.1 16.9 + + - -
150A GLN* 3.6 4.3 - - - -
165A ASP* 3.3 3.3 + - - -
169A HIS* 3.7 0.6 + - - -
209A MN 2.0 37.1 + - - -
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.9 11.4 - - - +
33A HIS* 3.4 17.0 - - - -
55A LEU* 5.6 1.5 - - - +
80A HIS* 2.8 38.1 + - - -
81A TYR* 3.8 4.5 - - - -
83A HIS* 1.3 78.4 - - - +
85A LEU* 1.3 61.6 + - - +
87A TRP* 3.6 6.4 + - - +
88A GLU* 3.2 31.4 + - - +
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Residues in contact with LEU 85 (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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81A TYR* 3.2 25.0 + - + +
82A CYS* 3.9 4.3 - - - +
84A SER* 1.3 77.8 - - - +
86A PHE* 1.3 65.4 + - - +
88A GLU* 3.1 16.9 + - - +
89A VAL* 3.1 31.9 + - + +
134A TRP* 4.0 8.1 - - + -
160A PRO* 3.8 32.8 - - + +
161A LEU 4.5 5.2 - - - +
162A LEU 4.6 7.2 - - - +
163A VAL* 3.8 20.4 - - + -
198A LYS* 4.0 26.0 - - + +
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Residues in contact with PHE 86 (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 ILE* 4.8 4.7 - - + -
28A HIS* 3.9 19.3 - + - -
82A CYS 3.0 18.6 + - - +
83A HIS* 3.4 9.6 - + + +
85A LEU* 1.3 77.6 - - - +
87A TRP* 1.3 90.5 + + - +
88A GLU 3.3 0.2 + - - -
89A VAL* 3.4 14.5 + - - +
90A MET* 3.5 39.6 - - + +
132A TYR* 5.5 1.6 - + + -
163A VAL* 3.5 26.4 - - + +
164A ILE* 4.7 0.2 - - + -
165A ASP* 3.7 37.0 - - + -
170A ALA* 5.3 1.1 - - + -
182A PHE* 4.8 10.3 - + - -
186A TRP* 3.4 29.6 - + - -
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Residues in contact with TRP 87 (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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7A PRO* 4.5 8.1 - - + -
8A LYS 6.0 0.7 - - - +
9A LEU* 3.3 30.3 - - + -
10A SER* 5.7 0.6 - - - +
11A TYR* 2.8 24.3 + - + +
25A LEU* 3.5 26.0 - - + -
28A HIS* 3.6 37.0 - + + -
29A HIS* 3.6 33.1 - + + -
33A HIS* 2.9 29.1 + + - -
83A HIS* 3.0 37.7 + + + -
84A SER* 3.6 6.7 + - - +
86A PHE* 1.3 98.7 - + - +
88A GLU* 1.3 62.7 + - + +
90A MET* 3.3 22.3 - - + +
194A ARG* 5.0 1.2 + - - -
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Residues in contact with GLU 88 (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 SER* 3.2 19.8 - - - +
85A LEU* 3.1 13.2 + - + +
87A TRP* 1.3 80.0 - - + +
89A VAL* 1.3 59.3 + - + +
90A MET 3.3 1.9 + - - +
191A ASN* 3.4 15.1 + - - -
194A ARG* 2.9 55.3 + - + +
198A LYS* 2.8 32.1 + - - -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.1 36.8 + - + +
86A PHE* 3.4 11.0 - - - +
88A GLU* 1.3 79.1 - - - +
90A MET* 1.3 60.9 + - + +
161A LEU 3.9 15.7 - - - +
162A LEU* 3.8 22.4 - - + -
163A VAL 4.0 19.3 - - - +
186A TRP* 4.8 0.9 - - + -
190A VAL* 3.4 9.7 - - - +
191A ASN* 2.8 27.9 + - - -
194A ARG* 4.5 9.0 - - + -
195A VAL* 4.3 9.6 - - + +
198A LYS* 5.2 1.3 - - + -
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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