Contacts of the helix formed by residues 38 - 46 (chain D) in PDB entry 6H2V
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN* 2.8 30.4 + - - +
73C GLY 4.0 11.9 + - - -
74C ALA 4.8 1.0 + - - -
75C GLY* 4.3 8.0 - - - -
36D GLU* 3.4 7.3 + - + +
37D PHE* 1.3 74.0 - - - +
39D PRO* 1.4 66.4 - - - +
40D ASN* 3.6 8.7 - - - +
41D PHE* 3.4 30.3 + - + +
42D VAL* 3.1 26.4 + - + +
85D HIS* 4.4 3.4 + - - +
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Residues in contact with PRO 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 3.5 46.6 - - + +
38D ASN* 1.4 82.4 - - - +
40D ASN* 1.3 65.7 + - + +
42D VAL* 4.1 2.8 - - + +
43D ALA* 3.1 27.0 + - - +
78D GLU* 6.3 0.4 - - + -
81D LEU* 4.1 13.9 - - + +
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Residues in contact with ASN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN* 3.1 26.8 - - - +
38D ASN* 3.6 12.1 - - - +
39D PRO* 1.3 82.3 - - + +
41D PHE* 1.3 57.7 + - - +
43D ALA* 3.8 4.5 + - - +
44D ARG* 3.2 30.4 + - - +
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN* 3.2 24.9 - - - +
53C LYS 3.8 13.9 - - - -
54C VAL* 4.0 3.6 - - + -
75C GLY* 3.6 41.1 - - - -
76C LEU* 3.8 4.3 - - + -
4D LEU* 3.8 22.7 - - + -
38D ASN* 3.4 29.7 + - + +
39D PRO 3.4 0.2 - - - -
40D ASN* 1.3 77.1 - - - +
42D VAL* 1.3 67.0 + - + +
44D ARG* 3.3 7.8 + - - +
45D MET* 3.1 64.7 + - + +
89D LEU* 4.1 21.1 - - + -
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.1 4.3 - - + -
38D ASN 3.1 19.0 + - - +
39D PRO* 4.1 3.8 - - + +
40D ASN 3.6 0.2 - - - -
41D PHE* 1.3 75.2 - - + +
43D ALA* 1.3 58.4 + - - +
45D MET* 3.0 23.1 + - - +
46D ILE* 3.0 21.0 + - + +
81D LEU* 3.3 39.9 - - + +
84D MET* 4.0 16.2 - - + -
85D HIS* 3.7 35.2 - - + +
88D LEU* 5.5 3.4 - - + -
89D LEU* 4.8 8.3 - - + -
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D PRO 3.1 18.7 + - - +
40D ASN* 3.9 5.4 - - - +
42D VAL* 1.3 76.3 - - - +
44D ARG* 1.3 56.5 + - - +
46D ILE 3.7 0.2 + - - -
47D PRO* 3.3 13.0 - - - +
74D TYR* 3.2 25.8 + - + -
75D GLU* 4.4 22.0 - - + +
81D LEU* 3.7 19.7 - - + +
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Residues in contact with ARG 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN* 2.9 30.0 + - - -
53C LYS* 3.8 13.6 - - - +
121C ASP* 2.8 43.8 + - - -
40D ASN* 3.2 21.0 + - - +
41D PHE* 3.5 11.4 - - - +
43D ALA* 1.3 78.3 - - - +
45D MET* 1.3 77.4 + - + +
47D PRO* 3.7 11.4 - - - +
48D LYS* 3.6 38.9 - - - +
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Residues in contact with MET 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 3.6 24.7 - - + -
121C ASP* 4.4 0.2 - - - +
150C ARG* 5.1 0.4 - - - -
4D LEU* 4.3 19.3 - - + -
8D LEU* 6.0 1.8 - - - -
41D PHE* 3.1 48.9 + - + +
42D VAL* 3.0 8.7 + - - +
44D ARG* 1.3 116.0 - - - +
46D ILE* 1.4 59.1 + - - +
47D PRO 3.4 0.7 - - - -
48D LYS* 2.9 37.9 + - + +
49D VAL* 3.1 23.8 + - + +
88D LEU* 5.0 7.4 - - + -
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.0 27.7 + - + +
43D ALA* 3.7 0.7 - - - +
45D MET* 1.4 75.3 - - - +
47D PRO* 1.4 64.3 - - + +
48D LYS 3.3 0.9 + - - -
49D VAL* 3.6 10.0 + - + +
51D TRP* 3.6 21.2 + - + -
70D PRO* 3.5 32.0 - - + +
74D TYR* 3.7 29.8 - - + -
80D PHE* 3.9 13.5 - - + -
81D LEU* 4.3 2.9 - - + -
84D MET* 3.7 43.3 - - + -
88D LEU* 4.6 6.7 - - + -
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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