Contacts of the helix formed by residues 80 - 93 (chain D) in PDB entry 3HR4
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 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530C ARG* 3.8 20.8 + - - +
75D LYS* 5.9 0.2 + - - -
78D ASP* 2.3 52.2 + - - +
79D THR 1.3 65.6 - - - -
81D SER* 1.3 59.3 + - - +
82D GLU* 2.9 6.5 - - - -
83D GLU* 3.1 26.9 + - + +
84D GLU* 3.5 10.9 - - - +
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Residues in contact with SER 81 (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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75D LYS 3.5 23.1 - - - -
76D MET* 4.7 7.4 + - - -
77D LYS* 4.7 2.2 - - - -
78D ASP* 4.0 7.4 + - - -
79D THR* 3.7 14.6 + - - -
80D ASP* 1.3 83.5 + - - +
82D GLU* 1.3 55.4 + - - +
83D GLU 3.2 0.2 - - - -
84D GLU* 3.5 14.3 - - - +
85D ILE* 2.7 48.8 + - - +
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Residues in contact with GLU 82 (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 THR* 3.4 20.3 + - + +
80D ASP* 4.5 0.4 - - - -
81D SER* 1.3 83.0 + - - +
83D GLU* 1.3 62.1 + - - +
85D ILE* 4.7 4.6 - - - +
86D ARG* 3.0 54.4 + - - +
138D TYR* 2.8 32.4 + - - -
142D VAL* 5.0 2.6 - - - +
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Residues in contact with GLU 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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530C ARG* 3.0 39.0 - - - +
80D ASP* 3.1 15.5 + - + +
82D GLU* 1.3 82.8 - - - +
84D GLU* 1.3 57.2 + - - +
86D ARG* 2.8 33.6 - - - +
87D GLU* 3.1 14.4 + - - +
90D ARG* 4.6 8.1 + - - -
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Residues in contact with GLU 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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523C LEU* 4.2 19.3 - - + +
526C CYS* 4.5 3.9 - - - +
527C MET* 3.7 25.1 - - + +
530C ARG* 2.9 35.4 + - - +
75D LYS* 3.7 40.7 + - - +
78D ASP* 4.9 0.2 - - - +
80D ASP* 3.5 23.2 - - - +
81D SER* 3.1 11.0 + - - +
83D GLU* 1.3 72.3 - - - +
85D ILE* 1.3 63.0 + - - +
86D ARG 2.9 4.5 - - - -
87D GLU* 3.0 21.5 + - - +
88D ALA* 3.2 10.7 + - - +
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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
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523C LEU* 4.4 20.6 - - + -
76D MET* 5.7 4.3 - - - -
81D SER* 2.7 34.6 + - - +
82D GLU* 5.0 2.9 - - - +
84D GLU* 1.3 73.2 - - - +
86D ARG* 1.3 61.1 + - - +
88D ALA* 3.4 5.9 + - - -
89D PHE* 3.1 18.2 + - - +
138D TYR* 3.7 18.1 - - - +
141D PHE* 3.4 28.5 - - + -
142D VAL* 4.2 22.7 - - + -
145D MET* 4.1 22.2 - - + -
146D THR* 4.9 9.2 - - + -
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Residues in contact with ARG 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 GLU* 3.0 38.9 + - - +
83D GLU* 2.8 26.0 - - - +
85D ILE* 1.3 78.6 - - - +
87D GLU* 1.3 59.1 + - - +
89D PHE* 3.2 13.1 + - - +
90D ARG* 3.0 60.2 + - - +
98D GLY* 6.3 1.2 - - - -
138D TYR* 3.3 49.7 - - - +
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Residues in contact with GLU 87 (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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526C CYS* 3.7 19.2 - - + +
529C MET* 5.4 0.9 - - - +
530C ARG* 2.6 56.9 + - - +
533C MET* 6.1 0.7 - - - +
83D GLU* 3.1 16.4 + - - +
84D GLU* 3.0 9.9 + - - +
86D ARG* 1.3 73.9 - - - +
88D ALA* 1.3 64.6 + - - +
90D ARG* 3.1 30.5 + - + +
91D VAL* 3.2 16.1 + - - +
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Residues in contact with ALA 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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522C VAL* 3.9 15.7 - - + -
523C LEU* 4.2 9.0 - - - -
526C CYS* 3.8 11.1 - - - -
84D GLU 3.2 11.3 + - - +
85D ILE 3.6 8.7 - - - +
86D ARG 3.3 0.2 - - - -
87D GLU* 1.3 76.0 - - - +
89D PHE* 1.3 63.7 + - - +
91D VAL* 3.1 13.2 + - - +
92D PHE* 3.3 17.7 - - - -
141D PHE* 3.7 17.0 - - + -
145D MET* 4.1 16.4 - - + -
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Residues in contact with PHE 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 ILE 3.1 12.4 + - - +
86D ARG* 3.4 16.8 - - - +
87D GLU 3.1 0.4 - - - -
88D ALA* 1.3 78.2 - - - +
90D ARG* 1.3 61.1 + - + +
92D PHE* 3.4 4.7 + - - +
93D ASP* 2.9 44.7 + - + -
98D GLY* 3.0 34.8 - - - -
100D ILE* 3.5 20.2 - - + -
136D VAL 3.5 17.7 - - - -
137D ASN 3.6 1.8 - - - -
138D TYR* 3.5 38.4 - + + -
141D PHE* 3.5 36.1 - + + -
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Residues in contact with ARG 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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83D GLU* 4.6 7.3 + - - -
86D ARG* 3.0 50.7 + - - +
87D GLU* 3.1 27.3 + - - +
88D ALA 3.1 1.2 - - - -
89D PHE* 1.3 80.4 - - + +
91D VAL* 1.3 67.8 + - - +
92D PHE 3.0 2.0 + - - -
93D ASP* 3.5 22.9 + - + +
94D LYS* 4.0 5.2 + - - +
96D GLY* 6.3 4.0 - - - -
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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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522C VAL* 3.7 11.0 - - + -
526C CYS* 3.6 22.0 - - - -
39D LEU* 3.6 48.5 - - + +
41D GLN* 4.4 8.1 - - + +
87D GLU 3.2 14.9 + - - +
88D ALA 3.1 7.3 + - - +
90D ARG* 1.3 77.9 - - - +
92D PHE* 1.3 62.8 + - + +
94D LYS* 3.2 27.9 - - - -
108D VAL* 3.9 11.9 - - + +
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Residues in contact with PHE 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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515C LEU* 4.5 4.9 - - + -
518C LEU* 3.8 26.9 - - + -
519C VAL* 4.2 7.2 - - + -
522C VAL* 3.9 24.9 - - + -
39D LEU* 6.1 0.4 - - + -
88D ALA 3.3 21.5 - - - -
89D PHE 3.4 1.1 + - - +
90D ARG 3.0 0.2 - - - -
91D VAL* 1.3 78.6 - - + +
93D ASP* 1.3 58.6 + - - +
94D LYS* 2.8 17.4 + - - +
100D ILE* 3.5 28.5 - - + -
104D GLU* 3.3 23.7 - - - +
105D LEU* 3.5 33.7 - - + -
108D VAL* 3.6 28.9 - - + -
141D PHE* 3.9 23.3 - + - -
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Residues in contact with ASP 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 PHE* 2.9 35.2 + - + +
90D ARG* 3.5 12.7 + - + +
92D PHE* 1.3 72.9 - - - +
94D LYS* 1.3 54.7 + - - +
95D ASP* 2.7 8.6 - - - +
96D GLY* 2.7 31.5 + - - -
97D ASN 2.9 5.3 + - - -
98D GLY* 2.7 28.5 + - - -
99D TYR 2.8 11.2 - - - +
100D ILE* 4.4 2.5 - - + -
104D GLU* 4.0 4.3 - - - -
203D CA 2.2 33.0 - - - -
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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