Contacts of the helix formed by residues 25 - 34 (chain B) in PDB entry 1MHQ
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 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B LEU* 1.3 82.2 + - - +
27B GLU* 3.2 7.1 - - - +
28B LEU* 3.3 26.5 + - - +
29B TRP* 3.7 16.6 + - - -
52B GLN* 3.6 24.9 + - - -
56B ASP* 5.0 3.0 + - - -
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Residues in contact with LEU 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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25B SER* 1.3 89.1 - - - +
27B GLU* 1.3 68.5 + - + +
28B LEU 3.2 0.2 + - - -
29B TRP* 3.4 1.7 + - - +
30B LEU* 2.8 27.2 + - - +
49B PHE* 3.5 20.7 - - + -
52B GLN* 4.2 19.5 + - + +
53B VAL* 4.8 6.5 - - + -
56B ASP* 4.2 15.9 - - - +
58B ASN 5.6 0.4 - - - +
59B GLY* 3.8 21.3 - - - +
62B HIS* 4.6 9.9 - - + -
63B ALA* 3.8 36.8 - - + +
66B LEU* 3.9 13.2 - - + -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 5.9 1.0 - - - +
74A PRO 4.5 2.8 - - - +
75A GLN* 3.5 48.9 - - + +
25B SER* 4.9 3.1 - - - +
26B LEU* 1.3 79.3 - - + +
28B LEU* 1.3 62.5 + - - +
30B LEU* 4.5 4.0 - - - -
31B ASN* 2.9 33.0 + - - +
66B LEU* 4.1 23.0 - - + +
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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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37A SER* 5.7 10.1 - - - -
25B SER* 3.3 20.2 + - - +
26B LEU 3.2 0.2 - - - -
27B GLU* 1.3 79.2 - - - +
29B TRP* 1.3 94.7 + - + +
31B ASN* 3.4 5.8 + - - +
32B LYS* 3.1 45.7 + - + +
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Residues in contact with TRP 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 SER* 3.7 17.5 + - - -
26B LEU 3.4 3.7 + - - +
28B LEU* 1.3 93.9 - - + +
30B LEU* 1.3 54.7 + - - +
32B LYS* 3.2 36.0 + - + +
33B ALA* 2.7 37.6 + - - +
45B ALA* 3.8 21.4 - - + +
48B ASN* 3.5 41.8 - - + +
49B PHE* 3.8 13.0 - - + -
52B GLN* 3.7 32.3 - - + +
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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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75A GLN* 5.1 3.1 - - - +
26B LEU 2.8 23.3 + - - +
27B GLU* 3.7 3.8 - - - +
29B TRP* 1.3 72.6 - - - +
31B ASN* 1.3 62.5 + - - +
33B ALA* 3.2 2.3 + - - -
34B THR* 2.8 49.7 + - + +
49B PHE* 3.4 25.4 - - + -
66B LEU* 3.6 45.8 - - + +
67B LEU* 4.0 22.2 - - + +
70B LYS* 4.2 12.3 - - + -
85B VAL* 4.2 9.9 - - + -
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Residues in contact with ASN 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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36A PRO* 3.8 17.2 - - + +
37A SER* 5.8 1.0 - - - +
75A GLN* 2.8 31.7 + - - -
27B GLU* 2.9 23.2 + - - +
28B LEU* 3.8 5.4 + - - +
30B LEU* 1.3 74.0 - - - +
32B LYS* 1.3 62.1 + - + +
34B THR* 3.4 5.2 - - - -
35B ASP* 2.8 33.0 + - - +
70B LYS* 2.6 31.7 + - - +
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Residues in contact with LYS 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 LEU* 3.1 34.4 + - + +
29B TRP* 3.2 41.9 + - + +
31B ASN* 1.3 77.7 - - - +
33B ALA* 1.3 63.2 + - - +
34B THR 3.3 0.2 + - - -
35B ASP* 3.4 16.9 + - - +
38B MET* 4.5 2.9 - - - +
42B ASP* 3.8 23.8 + - - +
45B ALA* 3.6 11.0 - - + -
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Residues in contact with ALA 33 (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 TRP 2.7 22.2 + - - +
30B LEU* 3.6 7.4 - - + +
32B LYS* 1.3 73.8 - - - +
34B THR* 1.3 57.3 + - - +
35B ASP 3.5 0.2 - - - -
41B GLN* 2.9 35.8 + - - +
42B ASP* 4.3 5.2 - - - -
45B ALA* 3.6 6.7 - - - +
46B ILE* 3.7 34.1 - - + +
49B PHE* 5.1 1.3 - - + -
81B TYR* 3.9 1.4 - - - +
85B VAL* 3.9 13.2 - - + -
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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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30B LEU* 2.8 38.9 + - + +
31B ASN 3.4 2.9 + - - -
33B ALA* 1.3 80.3 - - - +
35B ASP* 1.3 59.0 + - - +
36B PRO* 2.9 18.2 - - - +
70B LYS* 3.2 31.3 - - + -
78B GLU* 3.9 16.8 - - - +
81B TYR* 3.8 12.8 - - - -
82B ALA* 3.7 33.2 - - + +
85B VAL* 4.0 4.5 - - + -
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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