Contacts of the helix formed by residues 30 - 41 (chain A) in PDB entry 1AN7
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 ARG 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A SER* 1.3 74.2 + - - +
31A PHE* 1.3 60.9 + - - +
33A GLU* 3.1 12.2 + - - +
34A GLU* 3.0 33.1 + - + +
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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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6A ILE* 3.5 39.0 - - + -
29A SER* 3.8 6.3 - - - +
30A ARG* 1.3 80.2 - - - +
32A LYS* 1.3 64.2 + - - +
33A GLU 3.4 0.2 + - - -
34A GLU* 3.5 5.4 + - - +
35A ILE* 3.2 32.4 + - + +
85A ARG* 5.6 0.9 - - - -
113A SER* 4.1 13.7 - - - -
118A VAL* 3.6 29.4 - - + -
134A ILE* 3.7 32.8 - - + -
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Residues in contact with LYS 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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5A PRO* 3.7 36.3 + - - +
6A ILE* 3.8 18.6 - - + -
8A ASP* 4.9 4.8 + - - -
9A MET* 3.8 36.9 - - + +
26A VAL* 4.3 4.4 - - + +
27A PRO* 3.3 40.8 + - - +
28A ALA 5.1 0.2 - - - -
29A SER* 3.1 25.7 + - - +
31A PHE* 1.3 75.5 - - - +
33A GLU* 1.3 62.8 + - - +
35A ILE* 3.0 14.6 + - - +
36A LEU* 3.0 16.4 + - - +
59A LEU* 3.9 11.0 - - + -
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Residues in contact with GLU 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 SER 3.0 14.4 + - - +
30A ARG* 3.1 14.3 + - - +
32A LYS* 1.3 75.9 - - - +
34A GLU* 1.3 56.9 + - + +
36A LEU* 3.5 6.1 + - - +
37A ARG* 2.8 26.6 + - + +
48A TYR* 3.2 36.0 + - + +
50A ARG* 3.2 27.2 + - - -
59A LEU* 4.0 13.2 - - + +
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Residues in contact with GLU 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 ARG* 3.0 15.1 + - + +
31A PHE* 3.9 9.5 - - - +
32A LYS 3.3 0.2 - - - -
33A GLU* 1.3 75.3 - - + +
35A ILE* 1.3 63.0 + - - +
37A ARG* 3.1 37.2 + - + +
38A ILE* 3.3 25.8 + - - +
117A GLY* 4.8 4.6 - - - -
118A VAL* 3.7 38.2 + - + +
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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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6A ILE* 3.6 43.1 - - + -
9A MET* 4.0 16.2 - - + -
10A LEU* 4.8 6.1 - - + -
31A PHE* 3.2 20.4 + - + +
32A LYS 3.0 8.6 + - - +
34A GLU* 1.3 73.3 - - - +
36A LEU* 1.3 57.9 + - - +
38A ILE* 3.1 7.5 + - - +
39A LEU* 3.0 37.1 + - + +
111A ILE* 4.2 22.4 - - + -
118A VAL* 4.5 18.4 - - + -
134A ILE* 3.8 17.0 - - + -
135A CYS* 4.9 1.8 - - - -
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Residues in contact with LEU 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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9A MET* 4.3 13.9 - - - -
13A ILE* 4.0 24.5 - - + -
26A VAL* 5.0 0.2 - - + -
32A LYS 3.0 15.3 + - - +
33A GLU* 3.6 8.3 - - - +
35A ILE* 1.3 74.3 - - - +
37A ARG* 1.3 64.2 + - - +
39A LEU* 4.2 7.6 - - + -
40A ALA* 3.0 27.5 + - - +
45A ILE* 3.7 19.9 - - + +
48A TYR* 3.9 30.6 - - + -
59A LEU* 4.3 23.6 - - + -
61A VAL* 3.8 24.2 - - + -
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Residues in contact with ARG 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 GLU 2.8 17.3 + - - +
34A GLU* 3.1 37.1 + - + +
36A LEU* 1.3 76.9 - - - +
38A ILE* 1.3 63.2 + - - +
40A ALA* 3.8 2.5 - - - +
41A ARG* 3.2 53.2 + - - +
48A TYR* 3.9 23.5 - - + +
118A VAL 3.9 14.6 + - - -
123A GLU* 5.7 0.6 + - - -
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Residues in contact with ILE 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 GLU 3.3 8.3 + - - +
35A ILE* 3.1 8.7 + - - +
37A ARG* 1.3 79.1 - - - +
39A LEU* 1.3 66.9 + - - +
40A ALA 3.2 1.6 - - - -
41A ARG* 3.8 23.2 - - - +
42A GLU* 3.0 30.7 + - + +
109A ILE* 4.4 6.5 - - + -
111A ILE* 4.0 12.6 - - + -
118A VAL* 3.5 49.4 - - + +
119A LEU* 3.8 13.2 - - - +
120A THR* 3.6 25.6 - - + -
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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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10A LEU* 4.9 2.5 - - + -
13A ILE* 4.0 27.8 - - + -
35A ILE* 3.0 22.4 + - + +
36A LEU* 3.5 13.4 + - + +
38A ILE* 1.3 75.5 - - - +
40A ALA* 1.3 60.6 + - - +
42A GLU* 3.4 0.9 + - - -
43A GLY 3.2 4.2 + - - -
44A PHE* 2.8 48.6 + - + +
45A ILE* 3.6 17.5 - - + -
80A ILE* 5.2 3.8 - - + -
83A ILE* 4.6 17.3 - - + -
109A ILE* 5.3 1.8 - - + -
111A ILE* 3.8 28.5 - - + -
137A VAL* 4.4 15.0 - - + -
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Residues in contact with ALA 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 LEU 3.0 19.3 + - - +
37A ARG* 3.8 5.4 - - - +
39A LEU* 1.3 74.6 - - - +
41A ARG* 1.3 63.6 + - - +
43A GLY* 3.1 13.5 + - - -
45A ILE* 3.4 26.2 - - + +
46A LYS 4.5 3.6 - - - +
47A GLY* 4.2 16.6 - - - -
48A TYR* 4.8 5.8 - - + -
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Residues in contact with ARG 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 ARG* 3.2 37.4 + - - +
38A ILE* 3.5 28.9 + - - +
40A ALA* 1.3 77.0 - - - +
42A GLU* 1.3 94.0 + - - +
43A GLY 3.6 0.3 + - - -
120A THR* 4.5 1.0 - - - +
123A GLU* 2.8 42.6 + - - -
105B ARG* 4.0 9.5 + - - -
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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