Contacts of the helix formed by residues 25 - 37 (chain A) in PDB entry 2EYQ
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 ALA 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLY* 1.3 65.7 - - - -
26A ALA* 1.3 64.4 + - - +
27A CYS 3.7 0.7 - - - -
28A ALA* 3.2 2.9 - - - +
29A THR* 3.1 22.5 + - - +
58A GLU* 3.8 20.4 + - - +
62A PHE* 4.3 16.4 - - + -
430A ALA* 4.3 15.9 - - + -
431A GLU 5.8 0.2 - - - +
432A HIS 3.5 16.2 + - - +
433A GLY 4.1 2.6 + - - -
434A PHE* 3.8 13.2 - - + -
443A LEU* 4.4 10.8 - - + -
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Residues in contact with ALA 26 (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 LEU* 3.6 13.9 - - + -
23A THR 3.3 35.4 - - - +
24A GLY 2.3 19.6 + - - -
25A ALA* 1.3 63.0 - - - +
27A CYS* 1.3 68.5 + - - +
29A THR* 2.7 28.3 - - - +
30A LEU* 2.9 10.1 + - - +
355A PHE* 4.3 14.4 - - + -
434A PHE* 3.8 10.5 - - + -
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Residues in contact with CYS 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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22A LEU* 4.6 15.4 - - - +
23A THR 4.4 12.6 - - - -
24A GLY 3.8 2.9 + - - +
26A ALA* 1.3 74.4 - - - +
28A ALA* 1.3 69.9 + - - +
30A LEU* 2.7 20.6 + - - -
31A VAL* 2.8 20.0 + - + +
55A LEU* 5.0 12.3 - - + -
285A THR* 5.6 8.7 - - - +
339A LEU* 4.0 21.1 - - + -
341A THR* 6.0 4.7 - - - -
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Residues in contact with ALA 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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24A GLY 4.9 0.2 + - - -
25A ALA* 3.2 12.9 - - - +
27A CYS* 1.3 81.4 - - - +
29A THR* 1.3 61.7 + - - +
31A VAL* 3.4 3.3 + - - +
32A ALA* 3.2 18.0 + - - +
55A LEU* 5.3 5.2 - - + +
58A GLU* 3.5 41.2 + - + +
59A ILE* 4.1 17.8 - - - +
62A PHE* 3.8 15.5 - - + -
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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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25A ALA 3.2 10.1 - - - +
26A ALA* 2.7 26.2 + - - +
28A ALA* 1.3 79.5 - - - +
30A LEU* 1.3 61.8 + - + +
32A ALA* 3.4 5.9 - - - +
33A GLU* 3.3 32.8 + - - +
62A PHE* 3.5 28.8 - - - +
355A PHE* 4.5 12.1 - - + -
415A LEU* 5.1 9.7 - - - +
434A PHE* 3.7 21.9 - - + -
439A ARG* 4.5 6.9 + - - +
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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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7A TYR* 4.1 18.2 - - + +
19A LEU* 4.0 12.1 - - + -
22A LEU* 3.3 33.0 - - + -
26A ALA 2.9 9.6 + - - +
27A CYS* 2.7 16.3 + - - +
29A THR* 1.3 71.2 - - + +
31A VAL* 1.3 55.7 + - - +
32A ALA 2.9 1.6 - - - -
33A GLU* 2.9 11.2 + - - +
34A ILE* 2.7 45.2 + - + +
339A LEU* 4.0 17.3 - - + -
353A LEU* 3.2 37.2 - - + -
355A PHE* 4.7 6.1 - - + -
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Residues in contact with VAL 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 CYS* 2.8 24.9 + - + +
28A ALA* 3.9 3.4 - - - +
30A LEU* 1.3 71.8 - - - +
32A ALA* 1.3 62.1 + - - +
34A ILE* 3.9 9.4 - - - +
35A ALA* 3.3 21.5 + - - +
42A VAL* 4.9 8.4 - - + +
44A LEU* 3.7 37.9 - - + -
55A LEU* 5.7 1.3 - - + -
59A ILE* 3.9 15.9 - - + -
105A VAL* 4.1 18.3 - - + +
283A VAL* 4.5 9.4 - - + -
339A LEU* 4.1 19.1 - - + -
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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 ALA 3.2 10.7 + - - +
29A THR 3.4 10.8 - - - +
30A LEU 2.9 0.4 - - - -
31A VAL* 1.3 80.0 - - - +
33A GLU* 1.3 59.6 + - + +
35A ALA* 3.2 12.4 + - - +
36A GLU* 2.8 26.3 - - - +
59A ILE* 4.1 10.0 - - + +
62A PHE* 3.3 21.5 - - + +
63A THR* 3.0 25.5 + - - +
414A ARG* 5.9 0.4 - - - +
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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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5A TYR* 4.5 13.1 - - + -
7A TYR* 3.5 21.2 + - - +
29A THR* 3.3 16.2 + - - +
30A LEU* 2.9 13.8 + - - +
32A ALA* 1.3 75.9 - - + +
34A ILE* 1.3 54.7 + - - +
35A ALA 2.6 16.5 + - - -
36A GLU* 2.7 22.7 + - + +
37A ARG* 3.3 17.6 + - - +
414A ARG* 5.3 7.9 - - - +
439A ARG* 3.3 32.6 + - - -
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Residues in contact with ILE 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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7A TYR* 4.6 11.0 - - + +
9A LEU* 4.1 11.0 - - + -
19A LEU* 4.6 5.4 - - + -
30A LEU* 2.7 46.1 + - + +
31A VAL* 3.9 9.9 - - - +
33A GLU* 1.3 70.2 - - - +
35A ALA* 1.3 56.9 + - - +
37A ARG* 4.0 10.8 - - - +
38A HIS* 3.9 13.9 - - - +
42A VAL* 3.7 12.2 - - + +
281A LEU* 3.8 23.1 - - + +
283A VAL* 4.4 17.9 - - + -
337A VAL* 3.9 31.4 - - + -
339A LEU* 4.9 5.8 - - + -
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Residues in contact with ALA 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 VAL 3.3 12.4 + - - +
32A ALA* 3.2 12.5 + - - +
33A GLU 2.6 7.3 + - - -
34A ILE* 1.3 76.3 - - - +
36A GLU* 1.3 60.2 + - + +
37A ARG 3.5 1.6 - - - -
38A HIS 4.0 12.4 - - - +
40A GLY 4.6 2.3 - - - +
42A VAL* 4.0 9.9 - - + -
63A THR* 5.5 0.7 - - + -
65A GLN* 3.6 26.6 + - + +
103A ARG* 4.4 4.0 - - - +
104A GLY 5.0 5.0 + - - -
105A VAL* 3.6 24.0 - - + -
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Residues in contact with GLU 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 2.8 17.9 - - - +
33A GLU* 2.7 14.1 + - + +
35A ALA* 1.3 77.4 - - - +
37A ARG* 1.3 57.1 + - + +
38A HIS 3.6 0.7 - - - -
62A PHE 3.6 1.2 - - - +
63A THR* 2.8 34.4 + - - +
64A ASP* 5.1 0.7 - - - +
65A GLN* 4.7 9.9 - - + +
103A ARG* 3.6 18.3 + - - +
414A ARG* 2.8 41.2 + - - +
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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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5A TYR* 3.5 49.9 + - - +
7A TYR* 2.5 67.5 + - - -
8A THR* 3.7 8.9 - - - +
9A LEU* 2.7 50.1 - - + +
33A GLU* 3.5 17.5 - - - +
34A ILE* 4.0 2.7 - - - +
36A GLU* 1.3 77.1 - - - +
38A HIS* 1.3 57.1 + - - +
103A ARG* 5.1 0.2 - - - +
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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