Contacts of the helix formed by residues 45 - 57 (chain A) in PDB entry 1HMU
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 ASN 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU 3.3 1.8 + - - -
44A ARG* 1.3 90.7 + - - +
46A MET* 1.3 62.6 - - - +
47A ASP 3.4 2.5 - - - -
48A LYS* 3.3 30.7 + - + +
49A VAL* 3.1 32.7 + - + +
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Residues in contact with MET 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LYS* 5.3 1.8 - - - +
41A LYS* 3.4 28.0 - - + +
42A PRO 3.6 12.3 - - - +
43A LEU* 3.2 22.3 + - + +
44A ARG 3.0 4.2 - - - -
45A ASN* 1.3 78.6 - - - +
47A ASP* 1.3 62.2 + - - +
49A VAL* 3.3 4.7 + - - +
50A ALA* 3.0 28.8 + - - +
87A THR* 4.7 3.4 - - - +
90A GLN* 3.9 25.1 - - + +
91A ALA* 3.7 25.1 - - + +
94A GLU* 3.6 41.7 - - + +
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 4.6 4.9 + - - +
46A MET* 1.3 83.2 - - - +
48A LYS* 1.3 57.5 + - - +
50A ALA* 3.6 5.6 - - - +
51A GLU* 2.9 31.1 + - - +
91A ALA* 3.9 5.4 - - - +
96A ASP 3.9 4.3 - - - +
97A SER* 2.6 32.5 + - - -
98A HIS* 2.9 59.2 + - + +
99A TYR* 3.8 2.8 - - - -
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASN* 3.3 35.7 + - + +
46A MET 3.2 0.4 - - - -
47A ASP* 1.3 77.3 - - - +
49A VAL* 1.3 67.8 + - + +
51A GLU* 3.4 7.1 + - - +
52A LYS* 3.1 21.6 + - + +
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASN* 3.1 22.7 + - + +
46A MET* 3.8 4.3 - - - +
48A LYS* 1.3 78.9 - - + +
50A ALA* 1.3 62.3 + - - +
52A LYS* 3.1 20.8 + - + +
53A ASN* 3.2 21.1 + - - +
87A THR* 3.5 32.8 - - + -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A MET 3.0 18.2 + - - +
47A ASP 3.6 5.4 - - - +
49A VAL* 1.3 77.5 - - - +
51A GLU* 1.3 57.1 + - - +
53A ASN* 3.5 0.7 + - - -
54A LEU* 2.9 32.4 + - + +
87A THR* 3.8 18.8 + - - +
88A ILE* 4.1 11.6 - - + +
91A ALA* 3.8 26.9 - - + -
99A TYR* 4.0 10.1 - - + -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP 2.9 17.0 + - - +
48A LYS* 3.8 6.9 - - - +
49A VAL 3.3 0.2 - - - -
50A ALA* 1.3 76.3 - - - +
52A LYS* 1.3 58.3 + - - +
54A LEU* 3.8 2.4 - - + +
55A ASN* 2.8 34.8 + - + +
98A HIS* 5.0 9.0 + - - -
99A TYR* 3.0 26.6 + - + +
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 3.1 13.5 + - + +
49A VAL* 3.1 15.4 + - + +
51A GLU* 1.3 79.5 - - - +
53A ASN* 1.3 64.6 + - - +
55A ASN* 3.7 6.9 + - - +
56A THR* 3.2 23.4 + - + +
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 3.2 23.6 + - - +
50A ALA 4.2 0.7 - - - +
52A LYS* 1.3 85.0 - - - +
54A LEU* 1.3 61.2 + - - +
56A THR* 3.2 7.4 - - - +
57A LEU* 3.0 14.4 + - - +
63A TRP* 2.8 36.6 + - + -
84A GLN* 3.3 39.7 + - + +
87A THR* 3.0 25.0 + - - +
88A ILE* 4.1 10.8 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 2.9 19.2 + - + +
51A GLU* 3.8 4.5 - - + +
53A ASN* 1.3 74.4 - - - +
55A ASN* 1.3 65.0 + - - +
57A LEU* 3.3 19.1 + - + +
88A ILE* 3.8 31.6 - - + +
99A TYR* 3.4 39.5 - - + +
105A VAL* 3.6 18.2 - - + -
108A GLN* 3.5 45.4 - - + +
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Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.8 24.3 + - + +
52A LYS* 3.8 7.5 + - - +
53A ASN 3.3 0.2 - - - -
54A LEU* 1.3 80.2 - - - +
56A THR* 1.3 60.9 + - - +
57A LEU 3.8 2.3 + - - +
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS* 3.2 16.2 - - + +
53A ASN* 3.2 20.9 - - - +
55A ASN* 1.3 81.5 - - - +
57A LEU* 1.3 62.5 + - - +
58A GLN* 3.2 12.3 + - - +
62A SER 4.1 0.3 - - - +
63A TRP* 3.2 25.5 - - + +
64A LYS* 5.0 6.4 + - - +
65A ASP 5.9 0.3 + - - -
84A GLN* 5.2 0.4 - - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASN 3.0 14.4 + - - +
54A LEU* 3.3 20.1 + - + +
55A ASN 4.7 1.9 - - - +
56A THR* 1.3 76.1 - - - +
58A GLN* 1.3 68.9 + - - +
59A PRO* 3.9 0.7 - - - +
61A GLY* 3.6 33.9 - - - +
62A SER 3.9 2.2 - - - +
63A TRP* 3.6 32.5 - - + +
88A ILE* 4.7 4.0 - - + -
108A GLN* 3.5 52.2 - - + +
109A ILE* 5.7 0.2 - - - -
111A LYS* 5.8 0.4 - - + -
112A ALA* 4.5 4.3 - - + -
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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