Contacts of the helix formed by residues 38 - 47 (chain D) in PDB entry 3GZN
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 TRP 38 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLY 4.5 9.0 - - - -
33D ASP* 3.3 32.0 + - + -
36D GLY 3.3 0.6 - - - -
37D ARG* 1.3 117.3 - - + +
39D ASN* 1.3 58.8 + - - +
40D HIS* 3.1 4.0 - - - -
41D VAL* 2.9 22.5 + - + -
42D LYS* 2.9 36.4 + - + +
63D LEU* 3.7 35.2 - - + -
67D LEU* 3.6 31.9 - - + +
89D ALA 3.5 20.9 - - - -
90D LEU* 3.8 22.4 - - + -
92D GLY* 3.9 13.7 - - - -
93D PHE 5.6 0.4 - - - -
94D ARG* 4.3 2.5 - - - -
136D VAL* 5.4 1.8 - - + -
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Residues in contact with ASN 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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75C GLU* 2.8 32.5 + - + +
495C ALA* 4.8 0.2 - - - +
35D GLU* 5.4 3.2 + - - -
36D GLY* 3.2 31.8 + - - +
37D ARG 3.3 1.0 + - - -
38D TRP* 1.3 78.4 - - - +
40D HIS* 1.3 59.7 + - - +
41D VAL 3.2 1.6 + - - -
42D LYS* 4.0 23.9 + - - +
43D LYS* 3.4 38.8 + - - +
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Residues in contact with HIS 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLU* 3.3 50.1 + - + +
76C ASP* 4.7 4.9 - - - -
78C GLY 5.1 0.6 - - - -
79C ASN* 3.4 39.7 + - + +
494C ALA 4.9 2.0 + - - -
495C ALA* 3.7 11.8 - - - +
496C GLU* 2.9 44.9 + - + +
497C PRO* 4.2 11.2 - - + +
498C HIS 5.4 0.2 - - - +
37D ARG 4.8 1.9 + - - +
38D TRP 3.1 1.2 - - - -
39D ASN* 1.3 77.8 - - - +
41D VAL* 1.3 64.4 + - + +
43D LYS* 5.0 1.1 - - - -
44D PHE* 3.5 22.3 - - - -
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TRP* 2.9 26.9 + - + +
40D HIS* 1.3 87.8 - - + +
42D LYS* 1.3 67.2 + - - +
43D LYS 3.3 2.0 - - - -
44D PHE* 3.0 21.7 + - - +
45D LEU* 3.6 20.9 + - + +
63D LEU* 4.6 10.1 - - + -
66D LEU* 5.3 0.4 - - + -
90D LEU 4.1 19.7 - - - +
91D SER* 3.8 13.9 - - - +
329D PHE* 3.7 29.8 - - + -
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Residues in contact with LYS 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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37A SER* 6.3 0.8 - - - -
36D GLY 6.0 1.4 - - - +
37D ARG 6.2 0.2 - - - +
38D TRP* 2.9 20.8 + - - +
39D ASN* 4.0 25.8 + - - +
41D VAL* 1.3 77.7 - - - +
43D LYS* 1.3 59.1 + - + +
45D LEU* 2.9 6.6 + - - +
46D GLU* 2.8 68.4 + - + +
60D THR 6.0 1.1 - - - -
63D LEU* 3.6 33.2 - - + -
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Residues in contact with LYS 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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452C VAL* 3.5 26.3 + - - +
491C ARG* 3.7 11.3 + - - +
492C TYR 3.6 15.1 + - - +
493C GLY 3.1 25.2 + - - -
495C ALA* 4.4 8.2 - - + +
39D ASN* 3.4 28.1 + - - +
40D HIS* 5.8 0.8 - - - -
41D VAL 3.3 0.4 - - - -
42D LYS* 1.3 81.8 - - + +
44D PHE* 1.3 71.0 + - + +
46D GLU* 5.2 0.2 - - - -
47D ARG* 3.2 64.6 - - - +
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Residues in contact with PHE 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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164C GLY* 4.2 3.4 - - - -
165C LEU* 4.0 11.2 - - + -
491C ARG* 3.1 29.0 + - + +
492C TYR* 3.6 37.5 - + - -
495C ALA* 4.1 11.4 - - + -
497C PRO* 3.7 28.3 - - + -
40D HIS 3.5 26.0 - - - -
41D VAL* 3.0 12.7 + - - +
42D LYS 3.0 0.2 + - - -
43D LYS* 1.3 80.8 - - + +
45D LEU* 1.3 63.6 + - - +
56D PHE* 3.4 11.3 - - - -
329D PHE* 4.5 21.1 - + + -
335D ALA* 3.9 6.3 - - + +
336D TYR* 3.7 26.9 - + - -
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Residues in contact with LEU 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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41D VAL* 3.8 26.2 - - + +
42D LYS* 2.9 6.1 + - - +
44D PHE* 1.3 86.4 - - - +
46D GLU* 1.3 60.5 + - + +
47D ARG 3.5 1.1 - - - -
56D PHE* 3.7 8.8 - - + -
57D GLU 4.1 0.2 - - - +
58D PRO* 3.5 8.1 - - - +
59D SER 3.2 23.1 + - - +
62D SER* 3.8 22.9 + - - +
63D LEU* 3.7 38.8 - - + +
66D LEU* 4.8 7.9 - - + -
329D PHE* 4.1 9.0 - - + -
333D THR* 3.6 36.1 - - + +
335D ALA* 4.7 2.2 - - + -
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Residues in contact with GLU 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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454C ASN* 4.0 20.5 + - - +
42D LYS* 2.8 53.7 + - + +
43D LYS* 5.2 0.2 - - - -
45D LEU* 1.3 78.8 - - + +
47D ARG* 1.3 64.8 + - + +
58D PRO* 3.6 15.5 - - - +
59D SER 3.6 20.1 + - - +
60D THR* 4.1 29.7 - - + +
63D LEU* 6.5 1.1 - - + -
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Residues in contact with ARG 47 (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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451C GLY 2.7 30.0 + - - -
452C VAL 3.3 17.4 + - - -
453C SER 3.5 10.3 + - - -
454C ASN* 3.1 29.1 + - - +
457C VAL* 3.5 16.2 - - - +
490C CYS 3.4 6.3 + - - -
491C ARG* 2.8 66.1 + - + +
493C GLY* 3.9 1.0 - - - -
43D LYS* 3.2 39.2 + - - +
44D PHE 4.3 0.3 - - - +
46D GLU* 1.3 87.4 - - + +
48D SER* 1.3 66.6 + - - +
56D PHE* 3.4 11.2 - - - -
58D PRO* 4.5 0.7 - - - -
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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