Contacts of the helix formed by residues 81 - 92 (chain D) in PDB entry 4UQJ
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 81 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 2.8 28.7 + - - +
53D ALA 4.1 6.7 - - - -
55D SER* 3.8 11.0 - - - -
58D VAL* 3.9 19.3 - - - +
77D TYR* 3.7 6.8 - - - +
78D ASP* 3.0 18.3 + - - +
80D LYS* 1.3 75.3 - - - +
82D VAL* 1.3 64.0 + - - +
83D ASN 3.2 2.9 - - - -
84D THR* 3.0 22.3 + - - -
85D ILE* 3.3 8.8 + - - +
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D TYR* 3.5 42.2 - - + -
78D ASP 2.9 19.3 + - - +
79D LYS* 3.6 20.0 - - - +
81D SER* 1.3 78.5 + - - +
83D ASN* 1.3 77.1 + - - +
85D ILE* 3.4 3.1 + - - +
86D THR* 3.1 34.5 + - + +
101D PHE* 4.3 11.2 - - + -
103D THR* 4.3 8.3 - - + -
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Residues in contact with ASN 83 (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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55C SER* 3.6 9.3 + - - +
79C LYS 3.7 6.5 + - - -
80C LYS* 3.1 52.4 + - + +
83C ASN* 4.6 9.9 - - - +
79D LYS 4.9 3.0 + - - -
80D LYS 4.4 4.0 + - - +
81D SER* 3.2 0.6 - - - +
82D VAL* 1.3 86.6 - - - +
84D THR* 1.3 65.6 + - - +
86D THR* 3.1 9.7 + - - -
87D SER* 3.1 26.2 + - - -
107D HIS* 5.4 5.9 + - - -
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Residues in contact with THR 84 (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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55C SER* 4.4 8.7 + - - -
83C ASN* 5.8 0.5 - - - +
84C THR* 4.0 15.9 + - + +
55D SER* 4.1 21.0 + - - +
58D VAL* 4.6 9.4 - - + -
59D THR* 3.5 31.8 + - - +
62D PHE* 6.2 1.6 - - + -
80D LYS 4.8 1.0 + - - -
81D SER* 3.0 13.4 + - - -
83D ASN* 1.3 79.3 - - - +
85D ILE* 1.3 63.8 + - + +
87D SER* 3.7 0.2 - - - -
88D PHE* 3.0 48.4 + - + +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 4.6 8.3 - - + -
58D VAL* 3.5 27.8 - - + -
62D PHE* 4.7 15.3 - - + -
76D PHE 5.2 1.3 - - - +
77D TYR* 4.3 22.2 - - + -
81D SER 3.3 11.5 + - - +
82D VAL 3.4 6.3 + - - +
84D THR* 1.3 77.7 - - + +
86D THR* 1.3 65.7 + - + +
87D SER 3.0 0.3 + - - -
88D PHE* 5.0 1.6 - - - -
89D CYS* 2.9 35.8 + - + +
96D PHE* 3.5 55.2 - - + -
110D VAL* 5.3 1.8 - - + -
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D TYR* 5.3 1.8 - - + -
82D VAL* 3.1 20.6 + - + +
83D ASN* 3.1 17.7 + - - -
85D ILE* 1.3 77.6 - - + +
87D SER* 1.3 63.1 + - - +
89D CYS* 4.5 0.5 - - - +
90D GLY* 3.3 17.7 + - - -
103D THR* 3.8 28.7 - - + -
107D HIS* 3.8 37.8 + - + +
108D PRO* 4.7 5.4 - - - +
110D VAL* 4.4 16.2 - - + -
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Residues in contact with SER 87 (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 ASN* 2.6 28.8 + - - -
55C SER* 3.3 16.8 + - - -
56C PHE* 2.7 13.6 + - - +
83D ASN 3.1 16.9 + - - -
84D THR 3.7 2.0 - - - -
85D ILE 3.1 0.8 - - - -
86D THR* 1.3 80.4 + - - +
88D PHE* 1.3 66.1 + - - +
90D GLY* 3.1 2.8 + - - -
91D THR* 3.0 26.5 + - - -
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Residues in contact with PHE 88 (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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55C SER* 4.8 0.9 - - - -
56C PHE* 3.3 48.7 - + - -
59C THR* 3.6 33.4 - - + -
59D THR* 3.8 16.4 - - + -
62D PHE* 3.4 37.7 - + + -
63D CYS* 4.2 17.3 - - - -
84D THR* 3.0 47.0 + - + +
85D ILE* 4.1 1.3 - - - +
87D SER* 1.3 77.1 - - - +
89D CYS* 1.3 55.8 + - - +
91D THR 3.1 1.1 + - - +
92D LEU* 2.8 41.8 + - + +
315D CYS* 4.7 1.3 - - - -
316D LEU* 4.5 6.7 - - + -
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Residues in contact with CYS 89 (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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62D PHE* 3.5 26.2 - - - -
85D ILE* 2.9 29.0 + - - +
86D THR 4.5 2.2 - - - +
88D PHE* 1.3 77.5 - - - +
90D GLY* 1.3 56.9 + - - +
93D HIS* 3.2 5.2 + - - -
94D VAL* 3.0 47.2 + - - +
96D PHE* 3.5 29.6 - - + -
109D PHE* 3.3 18.6 - - - +
110D VAL* 4.8 3.1 - - + -
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Residues in contact with GLY 90 (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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86D THR 3.3 11.7 + - - -
87D SER 3.1 6.6 + - - -
88D PHE 3.1 0.6 - - - -
89D CYS* 1.3 79.8 - - - +
91D THR* 1.3 62.2 + - - +
93D HIS* 3.5 18.2 + - - -
108D PRO* 4.5 10.8 - - - -
109D PHE* 4.2 14.3 - - - -
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Residues in contact with THR 91 (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 ASN* 4.3 10.6 + - - -
56C PHE* 3.4 53.0 - - + +
87D SER 3.0 15.6 + - - -
88D PHE 3.8 2.5 - - - -
90D GLY* 1.3 77.4 - - - +
92D LEU* 1.3 62.0 + - + +
93D HIS* 3.2 4.9 + - - -
320D ALA* 4.5 8.7 - - + +
322D PRO* 3.4 25.5 - - + +
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Residues in contact with LEU 92 (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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56C PHE* 4.3 13.7 - - + -
62D PHE* 3.4 29.6 - - + -
66D PHE* 4.1 23.5 - - + -
88D PHE* 2.8 22.7 + - + +
91D THR* 1.3 80.3 - - + +
93D HIS* 1.3 71.1 + - - +
94D VAL* 3.0 18.5 + - + +
315D CYS* 3.8 36.3 - - + +
320D ALA* 4.3 13.2 - - + -
321D VAL 5.5 4.7 - - - +
322D PRO* 4.5 6.3 - - - +
323D TRP* 3.7 14.7 - - - -
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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