Contacts of the helix formed by residues 29 - 41 (chain A) in PDB entry 1ORN
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 ASN 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A HIS* 3.7 8.7 - - - -
28A ARG* 1.3 82.0 - - - +
30A PRO* 1.3 70.8 - - + +
31A PHE* 3.1 13.7 + - - +
32A GLU* 2.8 49.9 + - - +
33A LEU* 3.0 25.8 + - - +
60A ARG 5.5 4.2 + - - -
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Residues in contact with PRO 30 (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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27A HIS* 5.6 0.2 - - + -
29A ASN* 1.3 89.8 - - + +
31A PHE* 1.3 57.0 + - - +
33A LEU* 3.3 8.6 + - + +
34A LEU* 2.9 28.8 + - - +
105A VAL* 3.9 13.5 - - + +
126A VAL* 5.0 2.5 - - + +
130A ALA* 4.1 17.3 - - + +
131A PHE* 3.9 36.8 - - + -
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Residues in contact with PHE 31 (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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29A ASN* 3.1 11.0 + - - +
30A PRO* 1.3 76.4 - - - +
32A GLU* 1.3 71.8 + - + +
34A LEU* 3.3 3.6 + - + +
35A ILE* 3.1 37.3 + - + +
59A TYR 5.7 0.2 - - - -
60A ARG 3.6 17.7 - - - -
61A THR* 3.6 21.5 - - - -
62A PRO* 3.5 24.2 - - + -
65A TYR* 3.6 32.1 - + - -
93A LEU* 4.9 1.1 - - + -
94A CYS* 3.8 9.6 - - - -
97A LEU* 3.8 30.1 - - + -
105A VAL* 3.7 15.3 - - + +
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Residues in contact with GLU 32 (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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27A HIS* 3.6 7.9 - - + -
28A ARG* 2.6 59.9 + - - -
29A ASN* 2.8 32.3 + - - +
31A PHE* 1.3 83.4 - - + +
33A LEU* 1.3 63.1 + - - +
35A ILE* 3.5 0.4 + - - -
36A ALA* 3.0 24.8 + - - +
56A PHE* 3.3 48.7 - - + +
59A TYR 5.6 1.5 - - - +
60A ARG* 5.9 5.2 - - - +
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Residues in contact with LEU 33 (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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23A CYS* 4.5 13.9 - - - -
25A LEU* 4.8 6.1 - - + -
27A HIS* 3.8 35.4 - - + +
29A ASN 3.0 13.3 + - - +
30A PRO* 3.5 8.7 - - + +
32A GLU* 1.3 78.1 - - - +
34A LEU* 1.3 64.5 + - - +
36A ALA* 3.1 3.1 + - + +
37A VAL* 2.9 45.9 + - + +
125A VAL* 4.4 1.3 - - + +
126A VAL* 4.0 14.8 - - + -
129A VAL* 3.8 15.3 - - + -
130A ALA* 3.7 37.2 - - + +
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Residues in contact with LEU 34 (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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30A PRO 2.9 16.9 + - - +
31A PHE* 3.3 8.3 + - + +
33A LEU* 1.3 77.6 - - - +
35A ILE* 1.3 63.9 + - + +
37A VAL* 3.4 1.0 + - - +
38A VAL* 3.1 29.1 + - + +
93A LEU* 3.8 31.4 - - + -
97A LEU* 4.5 5.2 - - + -
105A VAL* 4.2 24.5 - - + -
112A LEU* 4.6 10.8 - - + -
115A LEU* 4.1 14.6 - - + -
118A VAL* 4.1 24.7 - - + -
122A THR* 4.5 2.9 - - + -
126A VAL* 3.9 25.8 - - + +
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Residues in contact with ILE 35 (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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31A PHE* 3.1 43.9 + - + +
32A GLU 3.9 3.6 - - - +
34A LEU* 1.3 77.5 - - + +
36A ALA* 1.3 64.3 + - - +
38A VAL* 3.2 6.6 + - + +
39A LEU* 3.0 38.6 + - + +
55A LEU* 4.2 3.8 - - + -
56A PHE* 4.0 14.8 - - + -
65A TYR* 3.8 24.2 - - + +
90A ILE* 4.0 36.8 - - + -
93A LEU* 4.6 15.9 - - + -
94A CYS* 4.6 0.4 - - - -
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Residues in contact with ALA 36 (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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25A LEU* 4.1 20.6 - - + -
26A VAL 4.7 5.6 - - - +
32A GLU 3.0 18.6 + - - +
33A LEU* 3.5 7.9 - - + +
35A ILE* 1.3 78.0 - - - +
37A VAL* 1.3 56.3 + - - +
39A LEU* 3.3 5.6 + - - +
40A SER* 2.9 26.9 + - - -
48A VAL* 3.8 18.1 - - + +
49A ASN* 6.1 0.2 - - - +
52A THR* 4.6 2.7 - - + -
56A PHE* 4.2 15.7 - - + -
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Residues in contact with VAL 37 (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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25A LEU* 3.8 10.5 - - + -
33A LEU* 2.9 46.0 + - + +
34A LEU 4.0 2.7 - - - +
36A ALA* 1.3 69.2 - - - +
38A VAL* 1.3 67.1 + - - +
40A SER* 3.1 20.2 + - - -
41A ALA* 3.6 4.2 + - - +
121A LYS* 4.1 16.4 + - - +
122A THR* 3.6 42.6 + - + +
125A VAL* 3.7 23.3 - - + -
126A VAL* 4.5 4.7 - - + -
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Residues in contact with VAL 38 (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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34A LEU* 3.1 20.5 + - + +
35A ILE* 3.6 10.1 - - - +
37A VAL* 1.3 77.2 - - - +
39A LEU* 1.3 64.1 + - - +
40A SER 3.4 0.2 + - - -
41A ALA* 3.5 12.9 + - - +
86A LYS* 3.6 21.8 - - + +
89A ASN* 5.3 4.3 - - + -
90A ILE* 4.5 21.3 - - + -
93A LEU* 4.1 14.6 - - + -
117A GLY* 4.2 20.6 - - - +
118A VAL* 4.0 27.1 - - + -
122A THR* 4.1 12.1 - - + -
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Residues in contact with LEU 39 (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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35A ILE* 3.0 30.7 + - + +
36A ALA* 3.6 7.6 - - - +
38A VAL* 1.3 77.1 - - - +
40A SER* 1.3 57.8 + - - +
43A CYS* 3.6 3.8 - - - +
48A VAL* 4.1 8.2 - - + +
51A VAL* 5.0 1.8 - - + -
52A THR* 4.0 26.0 - - + -
55A LEU* 4.1 11.9 - - + -
77A ILE* 4.1 22.7 - - + -
80A ILE* 3.3 31.9 - - + +
86A LYS* 2.7 36.6 + - + +
90A ILE* 3.8 22.9 - - + -
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Residues in contact with SER 40 (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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25A LEU* 4.1 12.3 - - - +
36A ALA 2.9 13.6 + - - -
37A VAL* 3.1 18.5 + - - -
39A LEU* 1.3 74.7 - - - +
41A ALA* 1.3 64.0 + - - +
42A GLN 3.1 3.3 + - - -
43A CYS 3.1 16.9 + - - +
45A ASP* 4.0 13.2 + - - -
48A VAL* 3.8 14.6 - - - -
121A LYS* 4.3 0.2 - - - -
18C PED 3.2 30.0 - - - +
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Residues in contact with ALA 41 (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 VAL 3.6 4.1 + - - +
38A VAL* 3.5 14.4 + - - +
39A LEU 3.2 1.6 - - - -
40A SER* 1.3 75.7 - - - +
42A GLN* 1.3 69.5 + - + +
43A CYS 3.3 0.2 + - - -
82A LEU* 4.1 1.3 - - + +
86A LYS* 2.7 32.1 + - - +
121A LYS* 5.7 0.2 - - - +
122A THR* 5.6 2.0 - - - +
18C PED 4.2 2.0 - - - +
19C G 3.5 40.2 - - - +
20C T 5.0 7.6 - - - +
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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