Contacts of the helix formed by residues 26 - 37 (chain A) in PDB entry 2ERY
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 GLY 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GDP 3.1 31.1 + - - -
24A GLY 3.3 0.6 + - - -
25A VAL* 1.3 80.5 - - - +
27A LYS* 1.3 60.1 + - - +
28A SER 3.3 2.2 - - - -
30A LEU* 2.9 40.8 + - - +
92A VAL* 4.9 0.2 - - - -
127A ASN* 3.6 9.4 - - - -
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Residues in contact with LYS 27 (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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1A GDP 2.8 27.7 + - - +
19A VAL* 3.7 24.1 - - + +
20A VAL 3.6 8.5 - - - +
21A GLY 3.2 30.8 + - - +
22A GLY 2.5 32.5 + - - -
23A GLY 3.6 2.6 - - - +
25A VAL* 3.7 12.0 - - + +
26A GLY* 1.3 76.4 - - - +
28A SER* 1.3 62.0 + - - +
30A LEU* 4.0 4.1 - - - +
31A THR* 2.8 29.8 + - - -
68A ASP* 3.4 12.3 - - - +
69A THR* 3.0 35.0 - - - +
70A ALA* 4.6 6.0 - - - +
92A VAL* 4.6 1.8 - - + -
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Residues in contact with SER 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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1A GDP 3.0 15.7 + - - -
3A MG 2.2 30.2 - - - -
27A LYS* 1.3 77.2 - - - +
29A ALA* 1.3 57.2 + - - +
31A THR* 3.2 1.0 + - - -
32A ILE* 2.9 37.3 + - - +
43A TYR* 3.4 30.1 - - - -
47A ILE 4.7 0.3 + - - -
68A ASP* 2.8 24.3 + - - -
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Residues in contact with ALA 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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1A GDP 2.7 46.1 + - + +
26A GLY 3.3 0.9 + - - +
28A SER* 1.3 73.0 - - - +
30A LEU* 1.3 58.4 + - - +
32A ILE* 4.0 0.5 - - - +
33A GLN* 3.0 34.3 + - - +
38A TYR 4.7 0.7 - - - +
39A PHE* 4.0 10.8 - - + -
40A VAL* 3.8 19.5 - - + +
158A ALA* 3.5 13.9 - - + -
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Residues in contact with LEU 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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19A VAL* 5.6 2.7 - - + -
26A GLY 2.9 23.4 + - - +
27A LYS* 4.0 3.8 - - - +
29A ALA* 1.3 72.1 - - - +
31A THR* 1.3 59.1 + - - +
33A GLN* 3.5 1.9 + - - -
34A PHE* 2.9 30.0 + - - +
90A LEU* 5.6 4.0 - - + -
92A VAL* 4.0 29.4 - - + -
125A ILE* 4.2 10.3 - - + -
127A ASN* 3.6 33.2 - - - +
156A ALA* 4.1 11.7 - - + -
158A ALA* 3.9 15.5 - - + +
164A VAL* 3.6 24.7 - - + +
168A PHE* 4.1 11.8 - - + -
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Residues in contact with THR 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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19A VAL* 3.9 16.8 - - - +
27A LYS 2.8 21.1 + - - -
28A SER* 3.6 3.4 - - - -
30A LEU* 1.3 78.2 - - - +
32A ILE* 1.3 57.4 + - - +
34A PHE* 3.2 6.6 + - - +
35A ILE* 3.0 37.6 + - + +
51A TYR* 3.5 39.0 - - + -
66A ILE* 4.0 17.2 - - + +
68A ASP* 3.8 15.7 - - + +
168A PHE* 4.4 5.3 - - - -
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Residues in contact with ILE 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 SER* 2.9 20.2 + - - +
29A ALA 4.2 2.0 - - - +
31A THR* 1.3 74.1 - - - +
33A GLN* 1.3 61.3 + - - +
35A ILE* 4.5 4.0 - - - +
36A GLN* 2.8 53.1 + - + +
37A SER 3.5 0.2 + - - -
38A TYR* 3.7 15.9 - - + +
40A VAL* 3.7 35.9 - - + -
43A TYR* 4.1 26.7 - - + -
51A TYR* 3.9 30.5 - - + +
68A ASP* 5.7 0.2 - - - +
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Residues in contact with GLN 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 ALA 3.0 20.0 + - - +
30A LEU* 3.7 4.7 - - - +
32A ILE* 1.3 77.5 - - - +
34A PHE* 1.3 59.2 + - - +
37A SER* 2.8 26.0 + - - -
38A TYR* 3.2 29.0 + - - +
39A PHE* 3.6 19.9 - - - +
158A ALA* 2.7 31.6 + - - +
159A LYS 4.0 5.1 + - - -
161A ARG* 2.9 48.6 + - + +
164A VAL* 4.0 14.1 - - + -
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Residues in contact with PHE 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 LEU 2.9 14.9 + - - +
31A THR 3.2 7.8 + - - +
33A GLN* 1.3 78.8 - - - +
35A ILE* 1.3 63.5 + - + +
37A SER* 5.1 0.3 + - - -
53A LYS* 2.7 63.0 + - + -
55A CYS* 3.8 8.3 - - - -
64A LEU* 3.8 16.6 - - + -
66A ILE* 3.4 34.5 - - + -
161A ARG* 3.6 6.9 + - - +
164A VAL* 3.6 5.1 - - + +
165A ASP* 3.4 30.3 - - + -
168A PHE* 3.5 43.5 - + + -
169A HIS* 4.5 5.8 - + - -
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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 THR* 3.0 22.7 + - + +
32A ILE* 4.3 1.3 - - - +
34A PHE* 1.3 90.4 - - + +
36A GLN* 1.3 73.1 + - + +
37A SER* 3.8 0.6 + - - -
51A TYR* 3.8 38.6 - - + -
52A THR 3.7 28.0 - - - +
53A LYS* 3.7 27.7 - - + +
66A ILE* 4.1 7.2 - - + -
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Residues in contact with GLN 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 ILE* 2.8 35.9 + - + +
35A ILE* 1.3 88.6 - - + +
37A SER* 1.3 69.0 + - - +
38A TYR* 3.2 14.5 + - + +
51A TYR* 4.6 17.0 - - - -
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Residues in contact with SER 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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32A ILE 3.5 0.2 + - - -
33A GLN* 2.8 34.7 + - - +
34A PHE 5.1 0.5 + - - -
35A ILE 3.8 0.8 + - - -
36A GLN* 1.3 74.1 - - - +
38A TYR* 1.3 58.0 + - - +
161A ARG* 3.4 25.5 + - - +
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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