Contacts of the helix formed by residues 23 - 32 (chain B) in PDB entry 4M83
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 SER 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B MET* 3.3 25.2 - - - +
19B HIS 4.8 4.9 + - - -
20B VAL 3.4 7.4 + - - -
21B ASN 3.3 0.2 - - - -
22B PRO* 1.3 78.2 - - - +
24B LEU* 1.3 65.3 + - - +
25B GLU 3.4 1.8 - - - -
26B VAL* 3.2 13.8 + - - +
27B ILE* 3.1 25.3 + - - +
39B TYR* 4.5 2.1 + - - -
110B ASP* 5.9 0.5 - - - +
130B LEU* 3.6 27.5 - - - +
191B LEU* 4.0 10.5 - - - -
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Residues in contact with LEU 24 (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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20B VAL* 3.3 21.4 + - + +
21B ASN* 3.2 33.7 + - + +
22B PRO 3.4 0.6 - - - -
23B SER* 1.3 75.2 - - - +
25B GLU* 1.3 81.2 + - + +
27B ILE* 3.1 22.0 + - - +
28B ARG 3.2 8.5 + - - -
48B LYS* 4.2 35.2 - - + +
49B VAL* 6.0 1.8 - - + -
52B THR* 3.9 17.1 - - + +
214B CYS 5.6 0.2 - - - +
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Residues in contact with GLU 25 (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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23B SER 3.4 0.4 - - - -
24B LEU* 1.3 101.1 - - + +
26B VAL* 1.3 61.1 + - - +
27B ILE 3.1 0.7 - - - -
28B ARG* 2.9 42.8 + - + +
29B GLU* 2.9 31.4 + - - +
52B THR* 5.7 1.6 - - - +
214B CYS* 3.2 11.6 - - - +
215B GLN 3.0 33.0 - - - +
216B GLY* 4.0 11.9 - - - +
217B ASP 5.4 0.2 + - - -
386B THR* 3.8 4.1 + - + +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 3.2 18.5 + - - +
25B GLU* 1.3 77.7 - - - +
27B ILE* 1.3 65.7 + - + +
29B GLU* 3.9 2.6 - - - +
30B LEU* 3.1 35.4 + - + +
130B LEU* 5.1 7.6 - - + -
191B LEU* 5.5 4.9 - - + -
214B CYS* 3.1 27.6 - - + -
386B THR* 4.3 8.7 - - - -
389B ALA* 4.0 25.8 - - + -
390B ALA* 4.5 5.6 - - - +
393B ILE* 3.9 27.4 - - + -
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Residues in contact with ILE 27 (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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11B MET* 4.1 18.6 - - + -
23B SER* 3.1 20.7 + - - +
24B LEU* 3.3 8.5 - - - +
25B GLU 3.1 0.4 - - - -
26B VAL* 1.3 78.8 - - + +
28B ARG* 1.3 65.7 + - - +
30B LEU* 3.1 18.9 + - + +
31B VAL* 3.1 13.7 + - - +
37B VAL* 4.2 10.3 - - + -
39B TYR* 4.1 24.5 - - + -
52B THR* 3.5 22.2 - - + +
54B ALA* 4.0 16.2 - - + -
108B LEU* 3.7 30.1 - - + -
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Residues in contact with ARG 28 (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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24B LEU 3.2 4.1 + - - +
25B GLU* 2.9 44.2 + - - +
26B VAL 3.4 0.2 - - - -
27B ILE* 1.3 78.2 - - - +
29B GLU* 1.3 59.2 + - - +
31B VAL* 3.1 5.9 + - - +
32B ALA* 2.9 30.1 + - + +
52B THR* 3.7 37.0 - - + +
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Residues in contact with GLU 29 (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 GLU 2.9 18.2 + - - +
26B VAL* 3.9 4.0 - - - +
28B ARG* 1.3 78.2 - - - +
30B LEU* 1.3 62.4 + - - +
32B ALA* 3.1 21.8 + - - +
33B ARG* 2.7 61.3 + - - +
386B THR* 4.0 15.3 - - - +
387B ARG* 5.1 3.6 - - - -
390B ALA* 4.1 12.8 - - + -
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Residues in contact with LEU 30 (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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9B ILE* 4.1 16.4 - - + -
26B VAL* 3.1 37.0 + - + +
27B ILE* 3.1 12.7 + - + +
29B GLU* 1.3 75.6 - - - +
31B VAL* 1.3 61.8 + - - +
33B ARG* 3.2 7.9 + - - +
34B GLY 3.7 2.6 + - - -
35B HIS* 3.1 46.6 + - + +
37B VAL* 4.2 13.9 - - + -
108B LEU* 4.0 23.3 - - + -
390B ALA* 3.9 31.6 - - + +
393B ILE* 4.1 9.9 - - + -
394B GLU* 4.6 1.6 - - + +
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Residues in contact with VAL 31 (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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27B ILE 3.1 14.5 + - - +
28B ARG 3.1 2.4 + - - +
30B LEU* 1.3 71.7 - - - +
32B ALA* 1.3 57.0 + - - +
33B ARG 3.1 8.3 + - - -
34B GLY* 3.5 10.6 + - - -
35B HIS 4.2 10.1 - - - +
37B VAL* 3.6 29.6 - - + +
52B THR 3.5 24.5 - - - +
53B GLY* 4.0 16.2 - - - +
54B ALA* 3.9 13.2 - - + +
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Residues in contact with ALA 32 (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 ARG* 2.9 19.7 + - + +
29B GLU* 3.1 23.4 + - - +
31B VAL* 1.3 74.6 - - - +
33B ARG* 1.3 59.2 + - - +
34B GLY 3.7 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