Contacts of the helix formed by residues 20 - 29 (chain B) in PDB entry 4MCA
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 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ILE* 6.4 0.7 - - + -
16B ASN 4.0 1.5 + - - +
17B ALA* 3.0 16.7 + - - +
19B ALA* 1.3 76.3 - - - +
21B VAL* 1.3 64.7 + - - +
22B GLY 3.2 3.6 + - - -
23B GLN* 3.5 14.3 + - - +
24B TYR* 3.2 30.7 - - + +
51B SER* 3.7 0.7 - - - -
55B HIS* 5.7 2.5 - - - -
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Residues in contact with VAL 21 (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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17B ALA 3.5 11.2 + - - +
18B LEU* 3.3 24.4 + - + +
20B ALA* 1.3 77.6 - - - +
22B GLY* 1.3 59.3 + - - +
24B TYR* 3.1 10.0 + - + +
25B ALA* 2.9 36.9 + - + +
48B LEU* 3.8 21.5 - - + -
51B SER* 3.3 2.6 + - - +
52B LEU* 4.3 2.7 - - + -
89B ILE* 4.9 2.5 - - + -
112B VAL* 4.9 9.4 - - + -
114B ILE* 4.0 24.7 - - + -
149B MET* 6.2 0.7 - - - -
151B VAL* 4.0 18.8 - - + -
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Residues in contact with GLY 22 (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 ALA 3.2 0.2 + - - -
21B VAL* 1.3 71.8 - - - +
23B GLN* 1.3 55.8 + - - +
25B ALA* 4.5 0.2 - - - -
26B LYS* 2.9 34.8 + - - +
51B SER* 2.6 36.6 + - - -
52B LEU* 4.0 17.5 - - - +
55B HIS* 3.6 10.1 - - - +
57B VAL* 4.2 1.1 - - - +
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Residues in contact with GLN 23 (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 ALA* 3.5 13.8 + - - +
22B GLY* 1.3 76.7 - - - +
24B TYR* 1.3 88.6 + - + +
26B LYS* 4.1 8.4 - - - +
27B SER* 4.2 6.9 + - - -
55B HIS* 3.4 32.5 - - + +
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Residues in contact with TYR 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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10B LYS* 4.4 18.2 - - + +
12B ILE* 3.6 34.4 - - + +
20B ALA* 3.2 34.3 - - + +
21B VAL* 3.1 7.6 + - - +
23B GLN* 1.3 100.1 + - + +
25B ALA* 1.3 64.3 + - - +
26B LYS 3.2 1.8 - - - -
27B SER* 2.6 27.9 + - - -
28B LEU* 3.8 1.6 + - - +
149B MET* 3.4 32.3 - - + +
151B VAL* 6.0 1.1 - - + -
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Residues in contact with ALA 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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21B VAL* 2.9 28.8 + - + +
22B GLY 4.0 2.7 - - - +
24B TYR* 1.3 79.3 - - - +
26B LYS* 1.3 60.4 - - - +
28B LEU* 3.1 8.1 + - - -
29B ALA 3.1 7.8 + - - +
32B TYR* 2.6 43.3 + - + +
52B LEU* 4.3 11.4 - - + -
57B VAL* 5.3 0.2 - - + -
89B ILE* 4.8 2.0 - - + -
112B VAL* 4.7 12.8 - - + -
149B MET* 4.4 1.7 - - - -
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Residues in contact with LYS 26 (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 GLY 2.9 20.3 + - - +
23B GLN* 4.1 8.1 - - - +
25B ALA* 1.3 77.3 - - - +
27B SER* 1.3 60.9 + - - +
28B LEU 3.2 1.0 + - - -
29B ALA 3.4 17.5 + - - +
30B ASP* 3.5 20.0 + - - +
55B HIS* 3.2 27.6 - - + +
56B GLY* 3.4 17.5 + - - -
57B VAL* 3.9 13.8 - - + +
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Residues in contact with SER 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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10B LYS* 5.3 5.7 + - - -
23B GLN 4.2 6.3 + - - -
24B TYR* 2.6 24.0 + - - -
26B LYS* 1.3 78.1 - - - +
28B LEU* 1.3 67.3 + - - +
149B MET* 4.6 4.9 - - - +
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Residues in contact with LEU 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 TYR 4.6 1.1 - - - +
25B ALA 3.1 2.0 + - - -
27B SER* 1.3 91.5 + - - +
29B ALA* 1.3 62.2 + - - +
32B TYR* 3.3 17.5 - - - +
110B PRO* 4.0 22.8 - - + +
112B VAL* 4.0 13.9 - - + -
148B ASP* 3.8 36.6 - - + +
149B MET* 4.0 23.1 - - + -
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Residues in contact with ALA 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 ALA 3.1 15.9 + - - +
26B LYS* 3.4 17.7 + - - +
28B LEU* 1.3 81.6 - - - +
30B ASP* 1.3 61.1 + - - +
31B HIS 3.5 2.2 - - - +
32B TYR* 3.5 23.2 - - + +
57B VAL* 4.3 1.6 - - - +
86B ARG* 3.6 35.7 - - + +
110B PRO* 4.4 2.2 - - + -
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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