Contacts of the helix formed by residues 86 - 105 (chain D) in PDB entry 5USJ
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 ASN 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ALA* 5.3 1.6 - - - +
12D ASP 4.7 8.3 + - - -
13D GLY 5.9 1.0 - - - -
14D VAL* 4.5 7.7 - - - +
83D ALA* 3.0 19.2 + - + +
84D ILE 3.4 1.2 - - - -
85D ASN* 1.3 82.1 - - - +
87D THR* 1.3 61.6 + - - +
88D LYS* 3.1 15.9 + - - +
89D SER* 2.7 56.9 + - - +
90D PHE 3.3 3.5 + - - -
124D THR* 3.7 0.6 + - - -
125D VAL* 4.2 2.1 - - - +
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Residues in contact with THR 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ASN 4.2 0.2 + - - -
86D ASN* 1.3 73.7 + - - +
88D LYS* 1.3 66.3 + - - +
90D PHE* 3.0 5.1 + - - +
91D GLU* 3.0 39.9 + - - +
124D THR* 3.2 39.8 + - - +
125D VAL* 4.0 9.6 - - + -
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Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA* 5.0 7.2 - - - +
12D ASP* 5.4 7.0 + - - -
86D ASN* 3.1 12.0 + - - +
87D THR* 1.3 82.7 + - - +
89D SER* 1.3 57.5 + - - +
91D GLU* 3.2 9.0 + - + +
92D ASP* 2.9 56.3 + - - +
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Residues in contact with SER 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA* 4.0 18.0 + - - +
14D VAL* 3.5 28.5 - - - -
81D VAL 5.0 0.7 - - - +
82D PHE* 3.6 6.0 - - - +
83D ALA 3.1 21.3 + - - -
86D ASN* 2.7 37.7 + - - +
88D LYS* 1.3 75.8 - - - +
90D PHE* 1.3 62.7 + - - +
92D ASP* 3.5 10.6 + - - +
93D ILE* 3.5 15.8 + - - +
96D TYR* 5.7 0.3 - - - -
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE* 3.7 41.7 - + + -
86D ASN 3.3 0.4 + - - -
87D THR* 3.0 9.0 + - - +
89D SER* 1.3 82.6 + - - +
91D GLU* 1.3 69.2 + - + +
93D ILE* 3.0 26.8 + - + +
94D HIS 4.6 0.7 + - - -
113D LEU* 4.6 1.1 - - + -
125D VAL* 3.7 21.8 - - + -
129D GLN* 3.9 39.7 - - + -
130D ALA* 3.8 21.5 - - + -
133D LEU* 3.7 35.0 - - + +
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Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D THR* 3.0 32.3 + - - +
88D LYS* 3.7 7.6 - - + +
90D PHE* 1.3 87.2 - - + +
92D ASP* 1.3 59.0 + - - +
94D HIS* 2.8 36.2 + - + -
95D HIS* 4.1 0.8 + - - -
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Residues in contact with ASP 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA* 3.7 15.3 - - + +
88D LYS* 2.9 49.9 + - - +
89D SER* 3.7 8.3 - - - +
90D PHE 3.2 0.2 - - - -
91D GLU* 1.3 77.9 - - - +
93D ILE* 1.3 64.2 + - - +
94D HIS 3.3 0.4 - - - -
95D HIS* 2.8 36.1 + - + +
96D TYR* 3.4 25.7 + - + -
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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
----------------------------------------------------------
10D GLY* 5.5 0.4 - - - -
80D CYS* 4.0 32.0 - - + +
81D VAL 3.9 24.7 - - - +
82D PHE* 4.1 6.3 - - + -
89D SER 3.6 10.3 - - - +
90D PHE* 3.0 26.6 + - + +
92D ASP* 1.3 77.4 - - - +
94D HIS* 1.3 64.6 + - - +
95D HIS 3.2 0.2 + - - -
96D TYR* 3.2 13.5 + - + +
97D ARG* 3.0 21.7 + - + +
113D LEU* 3.9 19.1 - - + -
133D LEU* 3.8 22.2 - - + -
137D TYR* 4.3 11.9 - - + -
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Residues in contact with HIS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE 4.6 0.4 + - - -
91D GLU* 2.8 26.1 + - + -
93D ILE* 1.3 79.1 - - - +
95D HIS* 1.3 95.4 + + - +
97D ARG* 3.3 2.1 + - - +
98D GLU* 3.0 52.7 + - - +
133D LEU* 5.2 5.5 - - + +
137D TYR* 3.2 26.0 + - - +
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Residues in contact with HIS 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 GLU 4.1 3.2 + - - -
92D ASP* 2.8 25.2 + - + +
94D HIS* 1.3 118.9 + + - +
96D TYR* 1.3 66.2 + - + +
97D ARG 3.0 1.4 + - - -
98D GLU* 3.2 15.9 + - - +
99D GLN* 3.1 26.5 + - - +
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Residues in contact with TYR 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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9D VAL* 4.0 26.7 - - + -
10D GLY* 3.4 36.9 + - - -
11D ALA* 3.4 22.6 - - - +
59D ALA 5.3 5.4 - - - -
60D GLY* 3.7 12.3 + - - -
71D TYR* 5.7 4.5 - - - -
72D MET* 4.6 6.0 - - + +
80D CYS* 5.0 5.6 - - + -
89D SER 5.7 0.2 - - - -
92D ASP* 3.4 40.4 + - + -
93D ILE* 3.2 12.9 + - + +
95D HIS* 1.3 79.5 - - + +
97D ARG* 1.3 57.2 + - - +
99D GLN* 3.5 15.0 - - - +
100D ILE* 3.0 35.8 + - + +
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Residues in contact with ARG 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D CYS* 5.3 2.2 - - - -
93D ILE* 3.0 18.0 + - + +
94D HIS* 3.6 5.6 - - - +
95D HIS 3.0 0.6 - - - -
96D TYR* 1.3 76.1 - - - +
98D GLU* 1.3 68.0 + - + +
99D GLN 3.1 2.0 - - - -
100D ILE* 3.4 3.8 + - - +
101D LYS* 3.3 54.3 + - + +
107D GLU 5.2 1.4 + - - -
109D VAL* 4.3 6.5 + - - +
111D MET* 3.5 45.7 - - - +
137D TYR* 3.2 69.3 + - + +
139D ILE* 3.9 19.8 - - - +
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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
----------------------------------------------------------
94D HIS* 3.0 47.3 + - - +
95D HIS* 3.2 20.5 + - - +
97D ARG* 1.3 80.6 - - + +
99D GLN* 1.3 58.3 + - + +
101D LYS* 3.6 9.9 + - - +
102D ARG* 3.1 27.5 + - - +
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Residues in contact with GLN 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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69D ASP* 4.6 5.6 + - - -
72D MET* 3.1 29.1 - - - +
95D HIS 3.1 16.3 + - - +
96D TYR* 3.5 14.0 - - - +
98D GLU* 1.3 77.4 - - + +
100D ILE* 1.3 67.2 + - - +
101D LYS 3.1 1.8 - - - -
102D ARG* 3.6 35.3 - - - +
103D VAL* 3.0 25.1 + - - +
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Residues in contact with ILE 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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9D VAL* 4.2 10.3 - - + -
72D MET* 3.7 22.0 - - + -
78D PHE* 3.7 48.0 - - + -
80D CYS* 4.1 13.5 - - - -
96D TYR* 3.0 21.3 + - + +
97D ARG 3.4 0.6 + - - +
99D GLN* 1.3 77.7 - - - +
101D LYS* 1.3 56.8 + - - +
103D VAL* 3.8 0.5 - - - +
104D LYS* 3.0 31.7 + - + +
109D VAL* 3.7 22.2 - - + -
111D MET* 3.5 30.5 - - + -
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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 ARG* 3.3 51.6 + - + +
98D GLU* 3.8 11.2 - - - +
99D GLN 3.1 0.6 - - - -
100D ILE* 1.3 75.2 - - - +
102D ARG* 1.3 57.3 + - - +
105D ASP* 2.6 30.5 + - - -
106D SER 3.1 25.1 + - - +
107D GLU* 2.6 49.4 + - - +
109D VAL* 4.4 13.0 - - + -
111D MET* 4.7 4.9 - - + -
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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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69D ASP* 3.1 26.9 + - - -
98D GLU 3.1 16.3 + - - +
99D GLN* 3.6 34.2 - - - +
101D LYS* 1.3 79.2 - - - +
103D VAL* 1.3 79.7 + - - +
105D ASP* 3.4 10.3 + - - +
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Residues in contact with VAL 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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69D ASP* 3.2 50.3 - - - +
72D MET* 3.4 23.3 - - + -
73D ARG* 3.2 37.9 + - - +
99D GLN 3.0 17.0 + - - +
102D ARG* 1.3 89.7 - - - +
104D LYS* 1.3 56.7 + - - +
105D ASP* 2.5 21.7 + - - +
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Residues in contact with LYS 104 (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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72D MET 3.0 24.0 + - - +
73D ARG* 2.8 40.0 + - - +
74D THR 4.3 1.0 + - - -
75D GLY 2.8 19.3 + - - -
76D GLU* 4.9 4.0 - - - +
78D PHE* 3.7 7.6 - - + -
100D ILE* 3.0 23.2 + - + +
101D LYS 4.1 1.6 - - - +
103D VAL* 1.3 75.3 - - - +
105D ASP* 1.3 68.8 + - - +
106D SER* 3.8 7.2 - - - +
109D VAL* 3.6 39.3 - - + +
110D PRO* 6.2 0.9 - - - -
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Residues in contact with ASP 105 (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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73D ARG* 5.6 0.2 - - - +
101D LYS 2.6 15.1 + - - -
102D ARG* 3.6 8.9 - - - +
103D VAL 2.5 15.3 + - - +
104D LYS* 1.3 76.0 - - - +
106D SER* 1.3 57.6 + - - +
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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
------------------------------------------------------------
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