Contacts of the helix formed by residues 27 - 40 (chain A) in PDB entry 1R00
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 LEU 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLY 3.4 8.2 + - - +
26A ASN* 1.3 73.1 - - - +
28A VAL* 1.3 68.6 + - + +
29A THR 3.6 0.4 - - - -
30A PRO* 3.4 16.5 - - + +
31A MET* 3.7 20.1 + - + +
124A THR* 5.4 12.6 - - + -
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Residues in contact with VAL 28 (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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26A ASN* 3.0 8.7 - - - +
27A LEU* 1.3 80.3 - - + +
29A THR* 1.3 66.2 + - - +
31A MET* 3.3 7.9 + - - +
32A ALA* 3.0 20.4 + - + +
72A HIS* 4.3 21.1 - - + +
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Residues in contact with THR 29 (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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22A LYS 5.3 1.6 - - - +
26A ASN* 2.8 25.2 + - - +
28A VAL* 1.3 74.4 - - - +
30A PRO* 1.3 68.2 - - + +
32A ALA* 2.9 4.7 + - - +
33A LEU* 2.9 42.2 + - + +
72A HIS* 2.9 32.9 + - + -
76A VAL* 4.1 20.9 - - + +
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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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26A ASN* 3.2 25.1 - - - +
27A LEU* 3.4 18.6 - - + +
29A THR* 1.3 94.5 - - + +
31A MET* 1.3 56.2 + - + +
33A LEU* 3.5 7.6 + - + +
34A ARG* 3.0 52.4 + - - +
110A LEU* 5.9 0.2 - - + -
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Residues in contact with MET 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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27A LEU* 3.7 21.0 + - + +
28A VAL* 3.3 11.0 + - - +
29A THR 3.2 0.8 - - - -
30A PRO* 1.3 76.0 - - + +
32A ALA* 1.3 60.2 + - - +
34A ARG* 3.3 23.2 + - + +
35A VAL* 2.9 38.6 + - + +
112A LEU* 4.3 12.6 - - + -
121A LEU* 3.7 33.4 - - + -
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Residues in contact with ALA 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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28A VAL* 3.0 13.4 + - + +
29A THR* 2.9 9.9 + - - +
31A MET* 1.3 77.2 - - - +
33A LEU* 1.3 56.5 + - - +
35A VAL* 3.3 2.7 + - - +
36A ALA* 2.9 28.8 + - - +
69A LEU* 3.6 29.2 - - + +
72A HIS* 4.0 17.9 - - - +
73A LEU* 3.9 17.7 - - + +
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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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29A THR* 2.9 33.1 + - + +
30A PRO* 3.8 11.4 - - + +
32A ALA* 1.3 73.0 - - - +
34A ARG* 1.3 66.2 + - - +
36A ALA* 3.3 3.8 + - - +
37A ALA* 2.9 24.4 + - - +
73A LEU* 3.8 17.0 - - + -
76A VAL* 4.8 1.3 - - + -
78A VAL* 3.8 28.9 - - + -
94A LEU* 5.7 3.6 - - + -
98A LEU* 3.9 36.1 - - + +
110A LEU* 4.2 17.3 - - + +
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Residues in contact with ARG 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* 3.0 46.5 + - - +
31A MET* 3.3 25.9 + - + +
33A LEU* 1.3 77.2 - - - +
35A VAL* 1.3 56.4 + - - +
37A ALA 3.4 0.5 + - - -
38A THR* 2.8 33.1 + - - -
109A TRP 5.6 1.2 + - - -
110A LEU* 3.4 36.4 - - + +
112A LEU* 4.0 17.9 - - + -
117A SER* 3.1 26.1 + - - +
120A ASP* 2.7 38.0 + - - +
121A LEU* 4.6 3.1 - - - -
307A ARG* 3.8 8.7 - - - +
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Residues in contact with VAL 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 MET* 2.9 26.5 + - + +
32A ALA* 3.7 6.3 - - - +
33A LEU 3.2 0.4 - - - -
34A ARG* 1.3 73.0 - - - +
36A ALA* 1.3 61.0 + - - +
38A THR* 3.7 2.7 - - - -
39A LEU* 3.0 42.9 + - + +
69A LEU* 3.9 24.0 - - + -
112A LEU* 4.1 19.1 - - + -
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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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32A ALA 2.9 17.4 + - - +
33A LEU* 3.7 7.6 - - + +
35A VAL* 1.3 74.3 - - - +
37A ALA* 1.3 65.0 + - - +
39A LEU 3.5 0.2 + - - -
40A ARG* 3.1 16.1 + - - -
41A LEU* 3.2 31.8 + - + +
42A VAL* 4.8 1.0 + - + -
69A LEU* 4.8 0.4 - - - +
73A LEU* 3.8 24.2 - - + -
78A VAL* 5.4 2.0 - - + -
98A LEU* 3.9 16.3 - - + +
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Residues in contact with ALA 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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33A LEU 2.9 11.6 + - - +
34A ARG 3.7 2.0 - - - +
36A ALA* 1.3 75.7 - - - +
38A THR* 1.3 57.5 + - - +
40A ARG* 2.9 19.3 + - - +
98A LEU* 3.8 12.9 - - + +
107A ARG* 3.0 53.8 + - + +
110A LEU* 3.6 26.2 - - + -
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Residues in contact with THR 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 ARG 2.8 18.8 + - - -
35A VAL* 3.7 5.4 - - - -
37A ALA* 1.3 75.9 - - - +
39A LEU* 1.3 64.1 + - + +
40A ARG* 3.5 8.1 + - - +
107A ARG* 4.3 3.1 + - - +
111A ASP* 3.8 18.7 - - - +
112A LEU* 3.0 40.7 + - + +
113A ASN* 4.4 17.5 + - - +
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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 VAL* 3.0 36.9 + - + +
36A ALA 4.0 0.9 - - - +
38A THR* 1.3 79.5 - - + +
40A ARG* 1.3 70.1 + - - +
41A LEU* 3.2 29.1 + - + -
44A HIS* 3.2 18.0 + - - -
59A THR* 3.6 17.9 - - + +
61A THR* 3.8 33.2 - - + -
66A LEU* 4.2 12.3 - - + -
69A LEU* 4.7 0.4 - - + -
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Residues in contact with ARG 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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36A ALA 3.1 1.5 + - - -
37A ALA* 2.9 13.2 + - - +
38A THR 4.1 4.9 + - - +
39A LEU* 1.3 79.4 - - - +
41A LEU* 1.3 59.4 + - - +
42A VAL 3.2 2.7 - - - -
43A ASP* 3.1 34.1 + - + +
44A HIS* 2.9 42.5 + - + -
98A LEU 5.8 1.1 - - - -
100A ASP* 3.3 29.3 + - - +
107A ARG* 3.5 42.1 - - - +
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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