Contacts of the helix formed by residues 103 - 118 (chain D) in PDB entry 2ORE
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 ASP 103 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D SER* 3.1 9.9 + - - +
102D GLN* 1.3 78.5 - - - +
104D PRO* 1.3 74.3 - - - +
105D PHE* 3.3 14.8 + - - +
106D ARG* 3.0 29.4 + - + +
107D ARG* 3.1 23.6 + - - +
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Residues in contact with PRO 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D SER* 4.0 17.7 + - - +
65D ILE* 3.7 7.1 - - + +
69D ARG* 6.3 0.7 - - - +
102D GLN 3.5 8.9 - - - +
103D ASP* 1.3 90.1 - - - +
105D PHE* 1.3 56.6 + - - +
107D ARG* 3.5 7.3 + - + +
108D ALA* 3.0 28.1 + - - +
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Residues in contact with PHE 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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65D ILE* 3.6 23.3 - - + +
69D ARG* 3.3 37.0 - - + +
72D GLU* 3.7 34.8 - - + -
73D TYR* 3.9 31.6 - + - -
76D ALA* 3.9 16.4 - - + -
103D ASP* 3.3 13.8 + - - +
104D PRO* 1.3 77.4 - - - +
106D ARG* 1.3 68.8 + - - +
108D ALA* 3.1 12.1 + - - +
109D VAL* 3.1 29.4 + - + +
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Residues in contact with ARG 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ALA* 5.4 2.4 + - - +
79D GLU* 4.9 6.3 + - - -
80D LEU* 4.3 20.8 - - - +
94D PHE* 5.0 7.9 - - - -
97D GLU* 2.6 41.5 + - - +
101D SER* 4.1 12.1 - - - +
103D ASP* 3.0 27.4 + - + +
105D PHE* 1.3 80.3 - - + +
107D ARG* 1.3 57.7 + - - +
109D VAL* 3.3 16.7 + - - +
110D LEU* 3.1 48.4 + - + +
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Residues in contact with ARG 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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58D ASP* 2.9 38.5 + - - +
98D PHE* 2.7 65.9 + - + -
99D ASN* 4.2 7.3 + - - +
101D SER* 3.4 41.1 + - - +
102D GLN* 4.7 2.0 - - - +
103D ASP 3.1 19.7 + - - +
104D PRO* 3.8 7.0 - - + +
106D ARG* 1.3 75.6 - - - +
108D ALA* 1.3 59.9 + - - +
110D LEU* 4.6 0.9 - - - -
111D PHE* 2.9 31.6 + - - +
125D TYR* 5.6 0.8 - - - -
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Residues in contact with ALA 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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58D ASP 5.9 0.9 - - - -
61D SER* 5.0 0.9 - - - +
62D LEU* 3.6 26.8 - - + +
65D ILE* 3.6 20.2 - - + -
73D TYR* 2.7 35.6 + - + -
104D PRO 3.0 14.6 + - - +
105D PHE 3.1 10.0 + - - +
107D ARG* 1.3 75.2 - - - +
109D VAL* 1.3 58.4 + - - +
111D PHE* 3.7 5.5 - - - +
112D LEU 3.6 7.6 + - - -
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Residues in contact with VAL 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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73D TYR* 3.7 18.8 - - + -
76D ALA* 3.5 47.8 - - + +
77D ALA* 3.9 6.7 - - - -
80D LEU* 3.8 18.8 - - + -
81D PHE* 5.9 0.2 - - - -
105D PHE* 3.1 25.0 + - + +
106D ARG* 3.5 19.1 - - - +
108D ALA* 1.3 76.7 - - - +
110D LEU* 1.3 67.4 + - - +
112D LEU* 3.2 15.2 + - - +
113D TYR* 3.4 9.9 + - - +
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Residues in contact with LEU 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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80D LEU* 3.6 26.0 - - + -
94D PHE* 3.8 28.7 - - + +
97D GLU* 3.8 21.1 - - - +
98D PHE* 3.6 46.4 - - + +
101D SER* 5.3 0.4 - - - -
106D ARG* 3.1 39.4 + - + +
107D ARG* 5.0 0.2 - - - -
109D VAL* 1.3 80.2 - - - +
111D PHE* 1.3 58.0 + - - +
113D TYR* 3.0 4.6 + - + +
114D LEU* 2.8 35.5 + - + +
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Residues in contact with PHE 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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8D LEU* 3.9 21.3 - - + -
10D TRP* 4.1 25.1 - + - -
56D ASN* 5.3 0.2 - - - -
58D ASP* 4.0 30.3 - - + +
59D LEU* 4.4 7.2 - - + -
62D LEU* 3.5 34.5 - - + -
98D PHE* 4.4 14.1 - + + -
107D ARG 2.9 21.9 + - - +
108D ALA* 3.7 8.1 - - - +
109D VAL 3.2 0.4 - - - -
110D LEU* 1.3 77.5 - - - +
112D LEU* 1.3 56.3 + - - +
114D LEU* 3.4 11.7 + - + +
115D ASN* 2.9 26.2 + - + +
123D CYS* 4.0 18.6 - - - -
125D TYR* 4.2 2.7 - - - -
131D PHE* 5.2 9.0 - + - -
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Residues in contact with LEU 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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7D PHE* 3.8 36.8 - - + +
8D LEU* 4.0 12.8 - - + -
62D LEU* 5.3 1.3 - - + -
73D TYR* 3.3 24.5 - - + +
77D ALA* 4.1 8.5 - - + -
81D PHE* 4.3 11.2 - - + -
108D ALA 3.6 1.2 + - - -
109D VAL 3.2 6.2 + - - +
111D PHE* 1.3 78.2 - - - +
113D TYR* 1.3 67.2 + - - +
115D ASN* 3.1 6.1 + - - +
116D ARG* 3.0 26.9 + - + +
143D PHE* 3.9 29.6 - - + -
144D PRO* 4.3 7.4 - - + -
148D LEU* 4.3 12.3 - - + -
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 3.7 37.5 - - + -
81D PHE* 3.9 12.0 - + + -
85D THR* 2.8 33.7 + - - -
90D VAL* 4.0 1.9 - - - +
91D TYR* 3.4 37.0 + + - +
94D PHE* 3.3 39.7 - + + -
109D VAL 3.4 2.5 + - - +
110D LEU 3.0 8.6 + - - +
112D LEU* 1.3 78.8 - - - +
114D LEU* 1.3 65.6 + - + +
116D ARG 3.3 0.3 + - - -
117D TYR* 2.8 71.4 + + + +
135D PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 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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91D TYR* 3.7 31.8 + - + +
94D PHE 4.8 0.9 - - - +
95D ARG* 4.0 26.2 - - + +
98D PHE* 3.9 36.1 - - + -
110D LEU* 2.8 22.2 + - + +
111D PHE* 3.6 8.3 - - + +
113D TYR* 1.3 87.9 - - + +
115D ASN* 1.3 60.1 + - - +
118D GLY* 2.9 29.5 + - - -
121D GLY* 5.3 0.2 - - - -
122D LEU 5.2 1.0 - - - +
131D PHE* 4.0 35.0 - - + -
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Residues in contact with ASN 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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7D PHE 4.4 1.4 - - - +
8D LEU* 2.9 30.8 - - + +
9D LYS* 2.6 55.7 + - - +
10D TRP* 4.8 5.4 - - - -
111D PHE* 2.9 17.5 + - + +
112D LEU* 3.1 9.9 + - - +
114D LEU* 1.3 77.9 - - - +
116D ARG* 1.3 62.3 + - + +
118D GLY 4.2 0.3 + - - -
121D GLY* 3.4 33.2 + - - -
122D LEU 5.0 3.9 + - - -
123D CYS* 6.0 0.4 - - - +
131D PHE* 5.6 1.3 - - - -
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Residues in contact with ARG 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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6D ALA 4.1 6.3 + - - -
7D PHE 2.8 34.6 + - - -
8D LEU 4.3 1.0 + - - -
9D LYS* 3.9 35.6 + - - +
81D PHE* 3.6 34.3 - - + -
112D LEU* 3.0 18.4 + - + +
113D TYR 4.0 0.4 - - - +
115D ASN* 1.3 81.9 + - - +
117D TYR* 1.3 63.3 + - + +
118D GLY 3.4 0.4 - - - -
138D TYR* 3.6 18.9 - - - -
141D PRO* 4.2 10.5 - - + +
142D TYR* 3.5 43.2 + - - +
144D PRO* 3.9 15.1 - - + +
147D GLU* 6.1 0.2 - - - -
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Residues in contact with TYR 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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80D LEU 4.3 0.2 - - - -
81D PHE* 3.5 44.1 + + - +
82D VAL 3.9 5.7 + - - -
85D THR* 3.7 4.5 - - - -
86D ASN* 3.2 43.2 - - + +
91D TYR* 3.6 19.1 - - + -
113D TYR* 2.8 56.0 + + + +
116D ARG* 1.3 78.8 - - + +
118D GLY* 1.3 59.6 + - - +
135D PHE* 3.7 12.8 - + + -
136D GLY* 3.1 21.1 + - - -
137D ARG 4.5 0.5 + - - -
138D TYR* 4.4 6.3 + - - -
141D PRO* 3.5 30.8 + - + +
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Residues in contact with GLY 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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91D TYR* 3.4 20.1 - - - -
114D LEU 2.9 20.7 + - - -
115D ASN 4.4 0.7 - - - +
116D ARG 3.4 0.6 - - - -
117D TYR* 1.3 80.8 - - - +
119D TYR* 1.3 67.0 + - - -
120D ASN 3.1 1.6 + - - -
121D GLY* 3.1 15.0 + - - -
122D LEU 6.0 0.4 - - - -
133D VAL* 4.4 3.6 - - - -
134D PRO 3.7 0.4 - - - -
136D GLY 3.7 1.6 - - - -
138D TYR* 3.2 13.3 - - - -
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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