Contacts of the helix formed by residues 77 - 97 (chain D) in PDB entry 5A0Q
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 THR 77 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ASN* 3.9 22.7 - - - +
73D PHE* 3.3 28.3 - - - -
75D GLY 3.9 3.0 + - - -
76D LEU* 1.4 66.6 - - - +
78D ALA* 1.4 65.8 + - - +
79D ASP 3.2 2.5 - - - -
80D ALA* 3.1 18.3 + - - -
81D ARG* 3.2 22.8 + - - +
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Residues in contact with ALA 78 (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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119C GLN* 3.5 24.2 + - - +
153C SER* 4.6 5.8 - - - +
154C GLY 2.8 32.3 - - - +
155C ASN* 5.2 0.2 - - - +
76D LEU* 3.2 5.6 - - + -
77D THR* 1.4 81.1 - - + +
79D ASP* 1.3 64.7 + - - +
81D ARG* 3.9 9.8 + - - +
82D ILE* 3.4 20.1 - - - +
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Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLN* 3.4 11.7 - - - +
123C GLN* 3.1 22.2 + - - +
76D LEU* 3.7 23.7 - - - +
77D THR 3.2 0.2 - - - -
78D ALA* 1.3 83.1 - - - +
80D ALA* 1.3 59.8 + - - +
81D ARG 3.4 0.9 - - - -
82D ILE* 3.2 8.1 + - - +
83D VAL* 3.0 28.8 + - - +
125D ARG* 3.1 30.4 + - - -
127D PHE* 4.3 5.9 - - + -
128D GLY* 3.3 15.1 + - - +
129D ILE* 3.8 10.5 - - + -
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D MET* 4.0 5.0 - - - +
73D PHE* 3.3 48.9 - - + -
76D LEU 3.3 1.2 + - - -
77D THR* 3.1 8.0 + - - +
79D ASP* 1.3 77.6 - - - +
81D ARG* 1.3 60.5 + - - +
83D VAL* 3.4 4.0 + - - +
84D ILE* 3.1 25.8 + - - +
129D ILE* 3.6 23.8 - - + -
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Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C THR* 3.8 8.5 + - - -
115C CYS* 2.8 47.7 + - - +
116C ASP* 2.9 24.5 + - - -
154C GLY* 3.9 13.5 - - - -
155C ASN* 4.5 2.3 - - - +
156C TYR* 3.7 36.8 + - - +
63D CYS* 6.1 0.2 - - - -
73D PHE* 4.7 4.9 - - + -
77D THR* 3.2 21.4 + - - +
78D ALA* 3.9 14.2 + - - +
80D ALA* 1.3 72.2 - - - +
82D ILE* 1.3 68.0 + - - +
84D ILE* 3.0 13.7 + - + +
85D ASN* 2.8 45.4 + - - +
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ASP* 3.0 45.5 - - + +
119C GLN* 3.8 17.5 - - + -
123C GLN* 5.5 3.1 - - + +
78D ALA 3.4 22.4 - - - +
79D ASP* 3.2 9.6 + - - +
81D ARG* 1.3 93.2 - - + +
83D VAL* 1.4 60.6 + - - +
85D ASN* 3.8 8.4 + - - +
86D ARG* 3.9 15.1 + - - +
127D PHE* 4.6 15.4 - - + -
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D MET* 4.4 4.9 - - + -
79D ASP 3.0 12.3 + - - +
80D ALA 3.6 7.4 - - - +
81D ARG 3.1 0.2 - - - -
82D ILE* 1.4 77.2 - - - +
84D ILE* 1.3 64.1 + - - +
85D ASN 3.3 0.3 + - - -
86D ARG* 3.3 6.6 + - - +
87D ALA* 3.1 17.8 + - - +
111D ILE* 4.0 27.4 - - + -
114D LEU* 4.2 14.5 - - + +
115D LYS* 4.7 2.7 - - + -
127D PHE* 3.3 45.5 - - + -
129D ILE* 3.7 25.8 - - + -
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Residues in contact with ILE 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D CYS* 3.2 41.7 - - + -
65D LEU* 3.7 35.2 - - + -
71D MET* 3.8 22.9 - - + -
80D ALA 3.1 11.3 + - - +
81D ARG* 3.0 25.9 + - + +
83D VAL* 1.3 75.7 - - - +
85D ASN* 1.3 59.3 + - - +
87D ALA* 3.3 3.7 + - + +
88D ARG* 2.9 53.8 + - - +
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Residues in contact with ASN 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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116C ASP* 4.1 13.0 - - - +
81D ARG* 2.8 30.2 + - - +
82D ILE* 3.8 18.1 + - - +
83D VAL 3.3 0.2 - - - -
84D ILE* 1.3 74.8 - - - +
86D ARG* 1.3 62.1 + - - +
88D ARG* 3.1 23.1 + - - +
89D VAL* 3.1 20.9 + - - +
70K ARG* 3.3 46.6 + - - +
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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 ILE 3.9 9.0 + - - +
83D VAL 3.3 8.4 + - - +
85D ASN* 1.3 76.0 - - - +
87D ALA* 1.3 63.1 + - - +
89D VAL* 3.4 32.1 + - - +
90D GLU* 3.1 25.2 + - - +
110D TYR* 3.2 29.4 + - - +
114D LEU* 4.0 18.8 - - + +
117D ARG* 5.7 1.6 - - - +
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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
----------------------------------------------------------
65D LEU* 3.4 20.6 - - + -
83D VAL 3.1 13.2 + - - +
84D ILE* 3.4 11.4 - - - +
85D ASN 3.2 0.2 - - - -
86D ARG* 1.3 78.1 - - - +
88D ARG* 1.4 54.3 + - - +
90D GLU* 3.3 11.5 + - - +
91D CYS* 3.1 30.1 + - - -
107D ILE* 5.0 1.1 - - + -
110D TYR* 4.6 7.4 - - + -
111D ILE* 3.6 26.7 - - + -
114D LEU* 4.9 0.4 - - + +
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D CYS* 4.0 19.0 - - - +
64D ALA 3.2 25.5 + - - +
65D LEU* 4.3 20.6 - - + +
84D ILE* 2.9 41.1 + - - +
85D ASN* 3.1 21.1 + - - +
87D ALA* 1.4 72.4 - - - +
89D VAL* 1.4 65.5 + - - +
90D GLU 3.2 0.2 - - - -
91D CYS* 3.2 17.3 + - - +
92D GLN* 3.2 20.0 + - + +
66K LEU* 3.8 14.8 - - + -
69K MET* 3.0 36.7 + - + +
70K ARG* 3.8 21.2 + - - +
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Residues in contact with VAL 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 ASN 3.1 9.2 + - - +
86D ARG* 3.6 34.8 - - - +
87D ALA 3.4 0.2 - - - -
88D ARG* 1.4 74.6 - - - +
90D GLU* 1.3 61.2 + - - +
92D GLN* 4.2 2.2 - - - +
93D SER* 2.9 39.5 + - - +
66K LEU* 4.2 16.8 - - + -
70K ARG* 3.4 24.2 - - - +
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Residues in contact with GLU 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 ARG* 3.1 17.3 + - - +
87D ALA* 3.4 8.9 - - - +
88D ARG 3.2 0.2 - - - -
89D VAL* 1.3 77.5 - - - +
91D CYS* 1.4 59.2 + - - +
93D SER* 3.7 5.0 + - - -
94D HIS* 3.2 16.8 + - - +
102D VAL* 3.9 2.8 - - - +
106D TYR* 3.2 32.4 - - + -
107D ILE* 3.2 28.1 - - - +
110D TYR* 3.1 50.9 - - + +
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Residues in contact with CYS 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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65D LEU* 3.7 25.1 - - - +
66D ASP* 3.2 38.1 - - - +
87D ALA 3.1 27.8 + - - -
88D ARG* 3.2 8.7 + - - +
90D GLU* 1.4 77.1 + - - +
92D GLN* 1.3 66.7 + - - +
94D HIS* 3.3 5.0 + - - +
95D ARG* 3.1 20.6 + - - +
102D VAL* 4.0 13.8 + - + +
107D ILE* 3.4 17.3 - - - -
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Residues in contact with GLN 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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65D LEU 4.8 4.0 - - - +
66D ASP* 4.1 13.9 - - - +
88D ARG 3.2 15.1 + - - +
89D VAL* 4.2 3.4 - - - +
91D CYS* 1.3 78.2 - - + +
93D SER* 1.3 65.0 + - - +
95D ARG* 3.3 20.8 + - - +
96D LEU* 3.3 17.3 + - - +
62K LYS* 3.4 61.4 + - + +
65K GLN* 3.5 23.9 + - - +
66K LEU* 3.9 20.6 - - + -
69K MET* 5.0 10.4 - - + +
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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 VAL* 2.9 31.8 + - - +
90D GLU* 4.0 5.8 - - - -
92D GLN* 1.3 74.8 - - - +
94D HIS* 1.3 59.5 + - - +
96D LEU* 3.6 7.2 + - - +
97D THR* 3.1 31.9 + - - +
62K LYS* 5.8 0.4 - - - -
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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
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90D GLU* 3.2 19.7 + - - +
91D CYS 3.5 5.4 - - - +
92D GLN 3.2 0.2 - - - -
93D SER* 1.3 77.2 - - - +
95D ARG* 1.3 58.8 + - - +
97D THR* 3.1 21.9 + - - -
98D VAL* 3.0 57.0 + - + +
100D ASP 3.8 6.3 + - - -
101D PRO 4.1 2.7 - - - -
102D VAL* 3.5 38.5 + - + -
103D THR 5.3 0.4 - - - -
106D TYR* 4.0 34.5 - + + +
66L TYR* 5.0 5.4 + - - -
70L ASN* 5.1 3.6 + - - -
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Residues in contact with ARG 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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66D ASP* 3.0 36.6 + - - +
67D ASP* 4.5 7.9 - - - +
68D ASN* 4.6 0.6 + - - -
91D CYS 3.1 11.1 + - - +
92D GLN* 3.3 25.1 + - - +
94D HIS* 1.3 75.4 + - - +
96D LEU* 1.3 56.4 + - - +
98D VAL 2.7 17.3 - - - +
99D GLU* 3.4 18.4 - - - +
100D ASP 3.8 11.2 - - - +
101D PRO* 3.7 34.4 - - + +
61K GLN* 6.3 1.1 - - - +
62K LYS* 3.9 23.6 - - + +
65K GLN* 6.6 0.2 - - - -
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Residues in contact with LEU 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 GLN 3.3 11.8 + - - +
93D SER* 3.9 9.2 - - - +
94D HIS 3.2 0.6 - - - -
95D ARG* 1.3 76.2 - - - +
97D THR* 1.3 71.0 + - + +
98D VAL 3.9 0.2 - - - -
99D GLU* 5.7 0.2 - - - -
55K GLN* 5.5 5.6 - - - +
58K GLU* 3.7 46.0 - - + +
59K TYR* 3.9 11.2 - - + +
62K LYS* 3.8 18.1 - - + +
81L LYS* 3.1 31.0 - - - +
85L ASN* 4.0 10.3 + - - +
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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
----------------------------------------------------------
93D SER* 3.1 18.2 + - - +
94D HIS* 3.1 19.5 + - - -
96D LEU* 1.3 88.1 - - + +
98D VAL* 1.3 68.8 + - - +
81L LYS* 3.3 21.3 - - - +
82L LEU* 3.3 23.5 + - - +
85L ASN* 4.1 11.5 + - - +
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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