Contacts of the helix formed by residues 32 - 43 (chain B) in PDB entry 4CRU
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 PRO 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1570A ALA* 4.6 6.7 - - + +
1574A GLU* 3.8 44.6 - - + +
30B SER 3.5 8.5 - - - +
31B SER* 1.4 85.5 - - - +
33B GLU* 1.3 67.1 + - + +
34B THR 3.3 0.8 + - - -
35B ARG* 3.8 27.0 + - + +
36B GLU* 4.7 2.6 + - - +
89B ARG* 4.7 13.8 + - - +
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Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B SER* 2.9 15.5 + - - +
32B PRO* 1.3 85.9 - - + +
34B THR* 1.3 66.2 + - + +
36B GLU 5.4 0.6 + - - -
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Residues in contact with THR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 2.7 52.7 + - + +
31B SER* 3.2 13.3 + - - +
33B GLU* 1.3 85.2 - - + +
35B ARG* 1.3 63.6 + - - +
36B GLU 3.5 2.4 + - - -
37B ASN* 3.7 9.6 + - - +
38B ALA* 3.3 18.0 + - - +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1571A VAL* 3.9 4.0 - - - +
1574A GLU* 5.3 0.2 - - - +
28B GLU 3.5 7.0 - - - -
29B LEU* 2.7 31.1 + - + +
30B SER 2.9 25.5 + - - -
31B SER 3.1 12.8 + - - +
32B PRO* 3.8 21.8 + - + +
33B GLU 3.6 1.2 - - - -
34B THR* 1.3 76.7 - - - +
36B GLU* 1.3 68.0 + - - +
38B ALA* 3.1 2.0 + - - +
39B LEU* 2.8 32.6 + - + +
65B ALA* 3.8 21.9 + - - +
66B LEU* 6.3 0.2 - - - -
68B GLN* 2.8 37.8 + - - +
69B GLU* 2.9 41.9 + - - -
72B ASN* 5.3 1.0 - - - +
89B ARG* 4.3 4.8 - - - +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO 4.7 2.9 + - - +
33B GLU 5.4 0.6 + - - -
34B THR 3.5 0.8 - - - -
35B ARG* 1.3 79.3 - - - +
37B ASN* 1.3 63.1 + - - +
39B LEU* 3.3 11.4 + - + +
40B LEU* 3.1 22.6 + - + +
85B HIS* 2.6 38.3 + - - -
89B ARG* 3.5 46.1 + - + +
92B ASN* 5.2 2.0 + - - +
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Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TRP* 4.0 21.2 - - - +
28B GLU* 4.6 5.5 + - - -
34B THR* 3.7 8.6 + - - +
35B ARG 3.3 0.4 - - - -
36B GLU* 1.3 80.3 - - - +
38B ALA* 1.3 63.7 + - - +
40B LEU* 3.2 14.8 + - - +
41B GLU* 3.0 36.4 + - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TRP* 3.3 45.3 - - + +
28B GLU* 4.1 7.4 - - + +
29B LEU* 3.7 12.1 - - + -
34B THR 3.3 15.2 + - - +
35B ARG 3.1 4.8 + - - +
37B ASN* 1.3 77.7 - - - +
39B LEU* 1.3 60.2 + - - +
42B LEU* 2.9 35.7 + - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.7 15.0 - - + +
35B ARG* 2.8 32.8 + - + +
36B GLU* 3.6 8.3 - - + +
38B ALA* 1.3 76.2 - - - +
40B LEU* 1.3 57.0 + - - +
42B LEU* 4.2 0.5 - - - +
43B SER* 3.0 34.1 + - - -
66B LEU* 3.6 31.6 - - + -
69B GLU* 4.1 22.0 - - + +
89B ARG* 4.1 25.4 - - + +
92B ASN* 3.8 13.3 - - + +
93B ALA* 3.9 10.1 - - + -
96B LEU* 3.8 14.0 - - + +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLU* 3.1 10.7 + - + +
37B ASN* 3.5 17.7 - - - +
39B LEU* 1.3 79.6 - - - +
41B GLU* 1.3 65.7 + - + +
43B SER* 2.9 19.6 + - - +
44B LYS* 3.5 33.9 - - + +
92B ASN* 3.8 21.9 - - - +
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B LYS* 5.7 0.5 + - - -
25B TRP* 3.4 55.2 + - + +
37B ASN* 3.0 34.1 + - - +
38B ALA 4.1 0.9 - - - +
40B LEU* 1.3 80.3 - - + +
42B LEU* 1.3 61.6 + - - +
44B LYS* 3.2 34.3 + - - +
45B LYS* 3.5 17.3 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 4.0 29.2 - - + +
25B TRP* 3.7 35.2 - - + +
26B ILE* 3.9 13.9 - - + +
29B LEU* 3.7 31.4 - - + -
38B ALA 2.9 21.4 + - - +
41B GLU* 1.3 72.6 - - - +
43B SER* 1.3 60.4 + - - +
45B LYS* 2.9 25.5 + - + +
46B ARG 3.6 4.9 + - - -
52B LEU* 3.9 13.6 - - + +
56B LEU* 4.5 3.1 - - + -
96B LEU* 3.8 25.0 - - + +
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 3.0 15.4 + - - -
40B LEU* 2.9 19.1 + - - +
42B LEU* 1.3 76.9 - - - +
44B LYS* 1.3 63.0 + - - +
45B LYS 3.4 0.9 + - - -
46B ARG* 3.0 27.9 + - - +
47B GLU* 3.8 4.2 - - - +
92B ASN* 3.5 26.7 + - - -
95B ALA* 4.4 4.9 - - - -
96B LEU* 3.9 9.8 - - - +
1801B GOL 3.5 19.9 + - - -
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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