Contacts of the helix formed by residues 38 - 46 (chain B) in PDB entry 6H2U
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 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ASN* 2.7 33.1 + - - +
73A GLY 4.2 8.3 + - - -
74A ALA 5.1 0.8 + - - -
75A GLY* 4.7 5.1 - - - -
36B GLU* 3.2 11.7 + - - +
37B PHE* 1.3 74.6 - - - +
39B PRO* 1.3 66.6 - - - +
40B ASN* 3.6 8.3 + - - +
41B PHE* 3.0 33.8 + - + +
42B VAL* 3.0 24.3 + - + +
85B HIS* 4.3 3.2 + - - -
89B LEU* 6.5 0.4 - - + -
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Residues in contact with PRO 39 (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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37B PHE* 3.4 48.7 - - + +
38B ASN* 1.3 85.9 - - - +
40B ASN* 1.3 63.0 + - - +
42B VAL* 3.8 3.0 - - + +
43B ALA* 2.9 31.8 + - - +
78B GLU* 6.1 1.6 - - + -
81B LEU* 4.1 14.7 - - + +
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Residues in contact with ASN 40 (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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52A ASN* 4.3 19.6 - - + +
38B ASN* 3.3 7.7 + - - +
39B PRO* 1.3 81.9 - - - +
41B PHE* 1.3 62.9 + - - +
43B ALA* 3.5 6.6 + - - +
44B ARG* 3.2 26.9 + - - +
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Residues in contact with PHE 41 (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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52A ASN* 3.3 25.1 - - - +
53A LYS 4.0 1.1 - - - -
54A VAL* 3.4 33.9 - - + -
75A GLY* 3.6 40.8 - - - -
76A LEU* 3.9 1.6 - - + -
4B LEU* 3.9 11.4 - - + -
38B ASN* 3.0 34.5 + - + +
40B ASN* 1.3 74.5 - - - +
42B VAL* 1.3 69.7 + - + +
44B ARG* 3.2 8.5 + - - +
45B MET* 3.0 48.9 + - + +
89B LEU* 4.1 25.1 - - + -
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Residues in contact with VAL 42 (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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37B PHE* 4.3 4.3 - - + -
38B ASN 3.0 16.4 + - - +
39B PRO* 3.4 5.4 + - + +
41B PHE* 1.3 82.7 - - + +
43B ALA* 1.3 63.5 + - - +
45B MET* 3.0 16.8 + - - +
46B ILE* 3.1 17.8 + - + +
81B LEU* 3.6 34.1 - - + +
84B MET* 4.1 12.1 - - + -
85B HIS* 3.8 39.7 - - + +
88B LEU* 5.3 4.7 - - + -
89B LEU* 4.7 4.3 - - + -
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Residues in contact with ALA 43 (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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39B PRO 2.9 18.1 + - - +
40B ASN* 3.7 7.2 - - - +
41B PHE 3.2 0.2 - - - -
42B VAL* 1.3 77.4 - - - +
44B ARG* 1.3 61.8 + - - +
45B MET 3.4 0.5 + - - -
46B ILE* 3.4 13.5 + - - +
47B PRO* 3.4 10.2 - - - +
74B TYR* 3.8 6.8 + - - -
75B GLU* 4.6 22.1 - - + +
81B LEU* 3.9 21.5 - - + +
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Residues in contact with ARG 44 (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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52A ASN* 3.0 31.2 + - - +
53A LYS* 3.7 15.6 - - - +
121A ASP* 2.9 42.6 + - - -
40B ASN* 3.2 18.1 + - - +
41B PHE* 3.3 12.6 - - - +
43B ALA* 1.3 79.6 - - - +
45B MET* 1.3 75.7 + - + +
47B PRO* 3.5 12.2 - - - +
48B LYS* 3.7 34.3 - - - +
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Residues in contact with MET 45 (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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54A VAL* 3.4 34.8 - - + -
150A ARG* 4.5 1.1 - - - +
302A EDO 3.5 16.4 - - - -
4B LEU* 4.1 22.6 - - + +
41B PHE* 3.0 35.4 + - + +
42B VAL* 3.0 11.9 + - - +
44B ARG* 1.3 105.5 - - + +
46B ILE* 1.3 66.3 + - - +
48B LYS* 2.9 34.1 + - + +
49B VAL* 3.3 15.5 + - + +
88B LEU* 5.1 7.0 - - + -
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Residues in contact with ILE 46 (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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42B VAL* 3.1 21.6 + - + +
43B ALA* 3.4 1.5 + - - +
45B MET* 1.3 76.4 - - - +
47B PRO* 1.3 71.2 - - + +
48B LYS 3.1 1.0 + - - -
49B VAL* 3.3 17.7 + - + +
51B TRP* 4.1 14.4 + - + -
70B PRO* 3.9 27.1 - - + +
74B TYR* 3.6 36.3 - - + -
80B PHE* 3.9 24.2 - - + -
81B LEU* 4.4 2.0 - - + -
84B MET* 4.1 29.8 - - + -
88B LEU* 4.8 5.6 - - + -
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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