Contacts of the helix formed by residues 83 - 99 (chain D) in PDB entry 3HW4
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 ASP 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D LYS* 6.2 0.2 - - - +
23D GLU* 3.5 16.6 - - - +
81D GLY 4.1 0.6 + - - -
82D ARG* 1.3 74.5 - - - +
84D ARG* 1.3 56.6 + - - +
85D THR* 4.3 8.3 - - - +
86D MET* 3.1 20.8 + - - +
87D ALA* 2.8 31.2 + - - +
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D GLU* 2.7 30.5 + - + +
24D TYR* 6.1 3.8 - - + -
82D ARG 3.7 0.6 + - - -
83D ASP* 1.3 70.2 - - - +
85D THR* 1.3 57.4 + - - +
87D ALA* 3.7 5.8 - - - +
88D TRP* 2.9 56.1 + - + +
106D LEU* 4.7 12.3 - - + -
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Residues in contact with THR 85 (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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83D ASP* 3.2 6.2 - - - +
84D ARG* 1.3 79.1 - - - +
86D MET* 1.3 54.3 + - - +
88D TRP* 3.9 3.8 - - - +
89D THR* 2.5 49.4 + - + +
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Residues in contact with MET 86 (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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82D ARG* 4.0 29.8 - - + +
83D ASP* 3.1 25.3 + - - +
85D THR* 1.3 81.0 - - - +
87D ALA* 1.3 57.4 + - - +
89D THR* 3.1 25.1 + - - +
90D VAL* 3.0 31.4 + - + +
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Residues in contact with ALA 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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79D ILE* 3.7 21.3 - - + +
82D ARG* 3.7 11.4 - - + +
83D ASP 2.8 19.4 + - - +
84D ARG 3.7 1.1 - - - +
86D MET* 1.3 72.2 - - - +
88D TRP* 1.3 58.7 + - - +
90D VAL* 2.7 29.1 - - - +
91D VAL* 3.0 12.3 + - - +
106D LEU* 3.5 31.9 - - + -
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Residues in contact with TRP 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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84D ARG* 2.9 48.1 + - + +
85D THR* 4.2 3.6 - - - +
87D ALA* 1.3 72.7 - - - +
89D THR* 1.3 58.2 + - - +
91D VAL* 3.7 24.0 - - + +
92D ASN* 2.8 39.6 + - - +
102D LYS* 4.1 23.8 - - + -
103D PRO* 3.4 27.8 - - + -
104D LYS 3.8 16.4 - - - -
105D PHE 4.3 0.4 - - - -
106D LEU* 3.4 42.4 - - + +
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Residues in contact with THR 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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85D THR* 2.5 47.2 + - + +
86D MET* 3.1 24.5 + - - +
88D TRP* 1.3 75.5 - - - +
90D VAL* 1.3 57.8 + - - +
92D ASN* 3.9 6.1 - - - +
93D SER* 3.0 28.6 + - - -
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Residues in contact with VAL 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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77D GLU* 3.5 35.9 - - + -
79D ILE* 4.0 14.6 - - + -
82D ARG* 4.0 22.0 - - - +
86D MET* 3.0 15.6 + - + +
87D ALA* 2.7 31.2 - - - +
89D THR* 1.3 73.3 + - - +
91D VAL* 1.3 64.7 + - - +
93D SER* 3.1 8.4 + - - +
94D ILE* 3.0 35.8 + - + +
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Residues in contact with VAL 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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79D ILE* 3.8 29.4 - - + -
87D ALA 3.0 17.8 + - - +
88D TRP* 3.7 22.9 - - + +
90D VAL* 1.3 75.6 - - - +
92D ASN* 1.3 64.7 + - - +
94D ILE* 3.2 7.6 + - - +
95D CYS* 2.9 27.2 + - - -
102D LYS* 4.4 3.1 - - + -
103D PRO* 3.8 29.6 - - + -
106D LEU* 4.1 5.8 - - + -
107D PRO* 4.1 16.8 - - + -
117D PHE* 4.1 6.1 - - + -
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Residues in contact with ASN 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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88D TRP* 2.8 29.6 + - - +
89D THR* 3.9 6.3 - - - +
91D VAL* 1.3 79.2 - - - +
93D SER* 1.3 62.4 + - - +
95D CYS* 3.2 4.9 + - - +
96D ASN* 2.8 34.9 + - - +
102D LYS* 2.7 43.4 + - - +
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Residues in contact with SER 93 (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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89D THR 3.0 15.4 + - - -
90D VAL* 3.1 17.5 + - - +
92D ASN* 1.3 75.6 - - - +
94D ILE* 1.3 63.4 + - - +
96D ASN* 3.1 13.8 + - - +
97D THR* 3.0 30.7 + - - -
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Residues in contact with ILE 94 (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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77D GLU* 4.2 9.0 - - + -
79D ILE* 4.4 3.6 - - + -
90D VAL* 3.0 38.1 + - + +
91D VAL 3.6 5.6 - - - +
93D SER* 1.3 76.0 + - - +
95D CYS* 1.3 58.9 + - - +
97D THR* 4.8 1.8 - - - -
98D THR* 2.8 45.7 + - + +
100D VAL* 5.6 0.4 - - + -
110D TYR* 3.7 62.8 - - + -
112D TYR* 3.8 17.0 - - - +
117D PHE* 3.9 16.8 - - + -
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Residues in contact with CYS 95 (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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91D VAL* 2.9 25.2 + - - +
92D ASN* 3.7 7.9 - - - +
93D SER 3.2 0.2 - - - -
94D ILE* 1.3 78.9 - - - +
96D ASN* 1.3 59.2 + - - +
98D THR* 4.5 0.2 - - - -
99D GLY* 2.8 31.0 + - - -
100D VAL* 3.4 24.5 - - - +
101D GLU 4.0 3.1 - - - -
102D LYS* 3.5 33.2 - - + -
117D PHE* 4.1 15.9 - - - -
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Residues in contact with ASN 96 (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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92D ASN* 2.8 21.6 + - - +
93D SER* 3.1 29.9 + - - +
95D CYS* 1.3 78.9 - - - +
97D THR* 1.3 65.4 + - - +
99D GLY* 4.2 3.7 + - - -
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Residues in contact with THR 97 (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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93D SER* 3.0 19.1 + - - -
94D ILE* 4.1 2.0 - - - -
96D ASN* 1.3 83.6 + - - +
98D THR* 1.3 70.7 + - + +
99D GLY 3.6 0.2 + - - -
112D TYR* 6.5 0.4 - - + -
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Residues in contact with THR 98 (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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94D ILE* 2.8 37.5 + - + +
97D THR* 1.3 82.2 - - + +
99D GLY* 1.3 57.5 + - - +
100D VAL* 3.2 28.8 + - - +
110D TYR* 3.5 12.1 + - - +
112D TYR* 4.2 17.7 - - + -
115D ASN* 3.9 19.5 - - - +
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Residues in contact with GLY 99 (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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95D CYS 2.8 18.0 + - - -
96D ASN* 4.0 3.1 - - - -
97D THR 3.3 2.4 - - - -
98D THR* 1.3 78.6 + - - +
100D VAL* 1.3 67.9 + - - +
101D GLU* 3.5 0.9 + - - -
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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