Contacts of the helix formed by residues 24 - 36 (chain G) in PDB entry 4U7B
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 THR 24 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G LYS 5.3 1.8 - - - +
23G LYS* 1.3 76.1 - - - +
25G ALA* 1.3 60.1 + - - +
26G ALA* 3.3 6.6 + - - +
27G GLU* 3.0 39.3 + - + +
28G SER* 2.6 33.7 + - - -
50G PHE* 4.0 2.0 - - - -
30I A 4.0 14.4 + - - +
31I A 3.3 18.5 + - - -
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G THR* 1.3 72.3 + - - +
26G ALA* 1.3 64.6 + - - +
28G SER* 3.0 5.7 + - - -
29G HIS* 3.0 21.8 + - - +
43G VAL* 4.4 2.7 - - - -
46G CYS* 4.2 6.9 - - - +
47G GLU* 3.6 39.9 - - + +
50G PHE* 3.9 23.2 - - + -
31I A 3.2 19.4 + - - +
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Residues in contact with ALA 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G THR* 4.0 2.9 - - - +
25G ALA* 1.3 74.6 - - - +
27G GLU* 1.3 60.7 + - - +
29G HIS* 3.5 2.9 + - - +
30G ARG* 3.1 32.9 + - - +
43G VAL* 3.5 22.8 - - + +
47G GLU* 5.5 0.2 - - - +
30I A 3.7 32.3 - - + +
31I A 2.7 20.2 + - - +
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Residues in contact with GLU 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LYS* 3.3 41.6 - - + +
24G THR* 3.0 35.9 + - + +
26G ALA* 1.3 75.2 - - - +
28G SER* 1.3 65.4 + - - +
30G ARG* 3.3 26.7 + - - +
31G MET* 3.1 30.4 + - + +
30I A 5.8 0.2 - - - +
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Residues in contact with SER 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 5.2 9.2 - - - -
18G CYS* 3.2 38.6 - - - +
23G LYS* 4.1 4.5 - - - +
24G THR 2.6 22.3 + - - -
25G ALA 3.5 4.3 - - - -
27G GLU* 1.3 73.4 - - - +
29G HIS* 1.3 54.5 + - - +
31G MET* 3.0 9.2 + - - +
32G LEU* 2.8 39.1 + - - +
46G CYS* 5.4 1.3 - - - -
50G PHE* 3.5 17.3 - - - -
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Residues in contact with HIS 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ALA 3.0 11.7 + - - +
26G ALA 3.6 8.7 - - - +
28G SER* 1.3 76.5 - - - +
30G ARG* 1.3 65.2 + - + +
32G LEU* 3.2 5.6 + - - +
33G VAL* 3.0 38.0 + - + +
40G VAL* 4.4 10.4 - - + +
41G PRO 3.2 28.0 + - - -
42G THR* 3.6 4.5 + - - -
43G VAL* 3.5 37.1 + - + +
46G CYS* 3.9 20.6 - - - -
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Residues in contact with ARG 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ALA* 3.1 25.1 + - - +
27G GLU* 3.6 31.2 + - - +
28G SER 3.2 0.4 - - - -
29G HIS* 1.3 83.1 - - + +
31G MET* 1.3 59.8 + - + +
33G VAL* 3.2 12.7 - - + +
34G GLU* 3.1 28.2 + - - +
30I A 2.8 41.8 + - - -
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Residues in contact with MET 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G PHE* 6.3 2.7 - - + -
18G CYS* 4.5 13.9 - - - -
21G LEU* 5.8 3.8 - - + -
23G LYS* 3.3 44.9 - - + +
27G GLU* 3.1 18.7 + - + +
28G SER* 3.0 12.6 + - - +
30G ARG* 1.3 74.1 - - + +
32G LEU* 1.3 61.6 + - + +
34G GLU* 3.5 15.3 + - - +
35G ALA* 2.9 30.8 + - - +
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Residues in contact with LEU 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G THR* 4.5 7.6 - - + +
14G VAL* 3.6 31.9 - - + -
15G LEU* 3.6 26.9 - - + -
18G CYS* 5.6 1.8 - - - -
28G SER 2.8 14.0 + - - +
29G HIS* 3.2 8.9 + - - +
31G MET* 1.3 73.2 - - + +
33G VAL* 1.3 60.9 + - - +
35G ALA* 2.8 23.8 + - + +
36G PHE* 3.2 31.3 + - + +
40G VAL* 4.1 26.7 - - + -
41G PRO* 4.5 9.9 - - + -
46G CYS* 3.9 20.0 - - - -
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Residues in contact with VAL 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G HIS* 3.0 26.5 + - + +
30G ARG* 3.2 25.1 - - + +
32G LEU* 1.3 76.9 - - - +
34G GLU* 1.3 61.8 + - - +
37G GLY* 3.5 33.3 + - - +
38G GLU* 4.1 20.0 - - + +
40G VAL* 4.2 9.1 - - + +
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Residues in contact with GLU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ARG 3.1 20.8 + - - +
31G MET* 3.5 15.5 - - - +
32G LEU 3.0 0.6 - - - -
33G VAL* 1.3 79.3 - - - +
35G ALA* 1.3 66.0 - - - +
36G PHE 4.7 1.7 - - - -
37G GLY* 5.4 0.2 - - - -
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Residues in contact with ALA 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G MET 2.9 17.0 + - - +
32G LEU* 2.8 11.6 + - + +
34G GLU* 1.3 76.5 - - - +
36G PHE* 1.3 83.6 + - + +
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Residues in contact with PHE 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G PHE* 4.7 23.0 - - + +
5G VAL* 4.2 37.0 - - + +
6G PRO* 5.5 9.9 - - + -
10G GLN 6.6 0.2 - - - -
11G THR* 5.4 9.6 - - - -
14G VAL* 4.8 17.5 - - + -
32G LEU* 3.2 33.8 + - + +
33G VAL 4.4 0.2 - - - -
34G GLU 4.7 0.9 - - - -
35G ALA* 1.3 94.2 - - + +
37G GLY* 1.3 60.2 + - - +
39G GLN 5.4 2.0 - - - +
40G VAL* 4.0 21.5 - - + -
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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