Contacts of the helix formed by residues 85 - 103 (chain D) in PDB entry 3O2Q
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 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D ASP* 2.5 36.0 + - - -
51D LYS* 5.7 1.8 - - - -
83D ASP* 2.6 21.3 + - - -
84D LYS* 1.3 72.2 - - - +
86D ILE* 1.3 64.2 + - - +
87D GLU 3.5 5.2 + - - -
88D VAL* 3.6 13.5 + - - +
89D ARG* 3.0 27.4 + - - +
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Residues in contact with ILE 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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84D LYS 3.6 4.7 + - - +
85D SER* 1.3 71.1 + - - +
87D GLU* 1.3 65.7 + - + +
89D ARG* 3.4 13.3 + - - +
90D LYS* 3.0 43.0 + - + +
122D ASN* 3.3 54.1 - - + +
124D ASN* 4.1 11.9 - - + +
125D VAL* 3.7 12.2 - - + +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ASP* 3.5 24.5 - - - +
52D ILE* 3.5 18.6 - - + +
85D SER* 3.2 2.4 + - - -
86D ILE* 1.3 82.8 - - + +
88D VAL* 1.3 60.3 + - - +
90D LYS* 3.0 36.6 + - - +
91D PHE* 2.9 27.7 + - - +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ASP* 4.5 3.1 - - - +
51D LYS* 3.8 24.2 - - + -
52D ILE* 4.3 11.0 - - + -
55D LEU* 4.7 7.6 - - + -
80D PHE* 3.6 28.5 - - + +
83D ASP* 3.6 34.5 - - + +
85D SER* 3.2 27.2 + - - +
87D GLU* 1.3 77.0 - - - +
89D ARG* 1.3 62.7 + - - +
91D PHE* 3.0 16.3 + - - +
92D VAL* 3.0 12.4 + - + +
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Residues in contact with ARG 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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80D PHE 4.4 2.2 - - - +
81D GLN* 2.9 30.5 - - - +
82D ALA 4.8 0.7 - - - -
83D ASP 2.8 36.9 + - - +
84D LYS* 3.4 23.6 + - - +
85D SER 3.0 8.9 + - - +
86D ILE* 3.8 26.1 - - - +
88D VAL* 1.3 74.9 - - - +
90D LYS* 1.3 63.5 + - - +
92D VAL* 3.1 13.0 + - - +
93D ILE* 3.0 27.3 + - - +
117D LEU* 4.6 7.6 - - + +
120D ASP* 2.7 43.0 + - - -
121D GLU* 4.6 11.8 + - - +
122D ASN* 4.0 3.0 - - - +
125D VAL* 3.9 14.3 - - + +
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Residues in contact with LYS 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 ILE* 3.0 31.7 + - + +
87D GLU* 3.0 38.9 + - - +
88D VAL 3.3 0.2 - - - -
89D ARG* 1.3 75.2 - - - +
91D PHE* 1.3 62.1 + - - +
93D ILE* 3.2 7.2 + - - +
94D GLY* 3.1 17.2 + - - -
124D ASN* 4.0 23.9 - - + +
125D VAL* 4.1 7.9 - - - -
128D LYS* 3.7 40.4 - - + -
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Residues in contact with PHE 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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52D ILE* 4.2 20.2 - - + -
55D LEU* 3.4 44.4 - - + -
56D LYS* 3.7 36.6 - - + -
59D GLN* 3.0 33.4 - - + -
77D ILE* 4.0 23.8 - - + -
80D PHE* 6.0 0.2 - - + -
87D GLU 2.9 14.3 + - - +
88D VAL* 3.0 12.1 + - - +
90D LYS* 1.3 74.6 - - - +
92D VAL* 1.3 73.0 + - + +
94D GLY* 2.9 4.7 + - - -
95D PHE* 2.9 25.6 + + + +
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Residues in contact with VAL 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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77D ILE* 4.0 6.7 - - + +
78D ILE* 4.3 23.1 - - + +
80D PHE* 3.6 37.7 - - + +
81D GLN* 3.8 23.1 - - + +
88D VAL 3.0 14.3 + - - +
89D ARG* 3.4 9.0 - - - +
91D PHE* 1.3 84.6 - - + +
93D ILE* 1.3 65.3 + - - +
95D PHE* 3.1 7.0 + - - +
96D ILE* 3.0 25.4 + - + +
117D LEU* 4.3 10.5 - - + -
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Residues in contact with ILE 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 ARG 3.0 12.4 + - - +
90D LYS* 3.6 7.0 - - - +
91D PHE 3.2 0.2 - - - -
92D VAL* 1.3 76.6 - - - +
94D GLY* 1.3 62.4 + - - +
96D ILE* 3.2 10.9 + - - +
97D GLU 3.1 16.8 + - - -
114D LEU* 4.3 7.9 - - + -
117D LEU* 3.6 27.6 - - + -
125D VAL* 3.5 42.6 - - + +
128D LYS* 3.9 19.7 - - + +
129D ALA* 3.7 12.8 - - - +
132D THR* 3.2 34.4 + - + +
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Residues in contact with GLY 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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59D GLN* 4.8 2.9 - - - -
90D LYS 3.1 9.0 + - - -
91D PHE* 2.9 8.9 + - - -
93D ILE* 1.3 75.3 - - - +
95D PHE* 1.3 56.3 + - - +
97D GLU* 3.2 10.1 - - - +
98D GLU* 3.0 33.6 + - - +
128D LYS* 4.0 18.1 - - - +
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Residues in contact with PHE 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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59D GLN* 3.5 43.2 - - + +
62D ILE* 4.0 12.3 - - + -
63D ILE* 3.9 14.4 - - + -
70D LEU* 3.9 20.6 - - + -
74D LEU* 3.7 27.1 - - + -
77D ILE* 3.5 41.7 - - + -
78D ILE* 4.4 10.3 - - + -
91D PHE* 2.9 16.8 + + + +
92D VAL* 3.3 11.7 - - - +
94D GLY* 1.3 74.8 - - - +
96D ILE* 1.3 63.9 + - - +
98D GLU* 3.2 2.8 + - - +
99D ALA* 2.8 33.5 + - + +
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Residues in contact with ILE 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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78D ILE* 3.9 26.5 - - + -
92D VAL* 3.0 19.3 + - + +
93D ILE* 3.4 9.0 - - - +
95D PHE* 1.3 78.5 - - - +
97D GLU* 1.3 63.2 + - - +
99D ALA* 3.2 3.4 + - - +
100D CYS* 2.9 38.3 + - - -
110D LEU* 4.3 18.2 - - + +
113D ASN* 4.3 16.4 - - + -
114D LEU* 3.8 37.5 - - + +
117D LEU* 4.3 23.1 - - + -
132D THR* 5.1 0.2 - - + -
136D LEU* 4.4 2.0 - - + -
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Residues in contact with GLU 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 ILE 3.1 7.9 + - - +
94D GLY* 3.2 11.1 - - - +
95D PHE 3.2 0.2 - - - -
96D ILE* 1.3 78.1 - - - +
98D GLU* 1.3 72.5 - - - +
100D CYS 3.4 0.2 + - - -
101D LYS* 3.1 43.6 + - - +
128D LYS* 4.0 12.3 + - - -
131D LEU 4.7 0.9 - - - +
132D THR* 2.9 41.7 + - + -
135D GLN* 3.2 30.0 - - + +
136D LEU* 3.8 12.5 - - + +
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Residues in contact with GLU 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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59D GLN* 3.8 15.7 - - - +
63D ILE* 3.7 27.9 - - + +
94D GLY 3.0 15.0 + - - +
95D PHE 3.7 0.9 - - - +
97D GLU* 1.3 95.3 - - - +
99D ALA* 1.3 61.4 + - - +
101D LYS* 3.3 20.9 + - - +
102D ARG* 3.2 21.5 + - - +
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Residues in contact with ALA 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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63D ILE* 3.7 14.7 - - + +
70D LEU* 4.1 23.8 - - + -
74D LEU* 5.2 0.4 - - + -
95D PHE* 2.8 28.8 + - + +
96D ILE* 3.9 5.2 - - - +
98D GLU* 1.3 72.8 - - - +
100D CYS* 1.3 57.9 + - - +
102D ARG* 3.4 3.7 + - - +
103D ASP 2.9 22.7 + - - -
106D LEU* 3.5 19.5 - - + +
110D LEU* 4.9 6.7 - - + -
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Residues in contact with CYS 100 (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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96D ILE* 2.9 29.4 + - - +
97D GLU 3.9 3.1 - - - +
99D ALA* 1.3 74.4 - - - +
101D LYS* 1.3 59.6 + - - +
102D ARG 3.1 1.3 - - - -
103D ASP 4.0 5.4 - - - -
104D ILE* 3.0 43.4 + - + +
106D LEU* 4.3 0.9 - - - -
107D LEU* 3.9 38.8 - - + -
110D LEU* 4.1 17.3 - - - -
136D LEU* 3.9 17.9 - - + -
139D VAL* 4.8 0.5 - - - +
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Residues in contact with LYS 101 (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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97D GLU* 3.1 41.5 + - - +
98D GLU* 3.3 23.7 + - - +
100D CYS* 1.3 76.0 - - - +
102D ARG* 1.3 62.2 + - - +
104D ILE 5.0 0.4 + - - -
135D GLN* 3.5 37.6 + - - +
136D LEU* 4.3 8.1 - - + -
139D VAL* 4.7 20.3 - - + +
206D ARG* 5.8 3.4 - - - +
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Residues in contact with ARG 102 (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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63D ILE* 3.3 24.8 + - + +
64D ASN* 3.1 25.3 + - - +
67D PRO* 3.2 33.4 - - + +
70D LEU* 3.9 22.7 - - + -
98D GLU 3.2 12.0 + - - +
99D ALA 3.6 6.5 - - - +
100D CYS 3.1 0.4 - - - -
101D LYS* 1.3 82.7 - - - +
103D ASP* 1.3 63.4 + - + +
104D ILE 4.0 0.8 + - - -
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Residues in contact with ASP 103 (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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70D LEU* 5.0 1.3 - - + -
71D ASP* 4.5 6.2 - - - +
99D ALA 2.9 7.6 + - - +
100D CYS* 3.4 4.0 - - - +
102D ARG* 1.3 85.9 - - + +
104D ILE* 1.3 51.5 + - - +
105D GLU* 3.5 26.1 + - - +
106D LEU* 2.8 64.4 + - + +
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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
------------------------------------------------------------
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