Contacts of the helix formed by residues 76 - 95 (chain A) in PDB entry 3DEW
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLN* 3.1 14.7 + - - +
75A GLY* 1.3 79.5 - - - +
77A PRO* 1.4 66.9 - - - +
78A LEU* 3.4 11.6 + - - +
79A ALA* 3.0 36.3 + - + +
80A VAL* 3.0 11.7 + - - +
138A ARG* 4.7 0.4 - - - +
204A CL 4.5 0.2 - - - -
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Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLY 3.9 0.4 - - - -
76A ASP* 1.4 86.0 - - - +
78A LEU* 1.3 63.2 + - - +
80A VAL* 3.2 3.3 + - + +
81A MSE 3.0 29.8 + - + +
131A SER* 3.2 34.5 - - - +
134A ALA* 5.0 1.1 - - + -
135A GLY* 4.1 14.1 - - - +
138A ARG* 3.3 24.9 - - - +
140A LEU* 4.3 8.1 - - + -
141A PHE* 3.6 26.9 - - + -
204A CL 3.8 8.9 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASP* 3.2 9.7 + - - +
77A PRO* 1.3 78.6 - - - +
79A ALA* 1.3 58.2 + - - +
81A MSE 3.2 8.1 + - + +
82A THR* 2.9 46.2 + - - +
140A LEU* 6.0 0.4 - - - +
141A PHE* 4.8 7.0 - - + -
187A VAL* 3.7 23.6 - - + -
191A THR* 4.6 18.4 - - + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 3.5 27.6 - - + +
76A ASP* 3.0 31.3 + - + +
78A LEU* 1.3 76.2 - - - +
80A VAL* 1.3 59.9 + - - +
82A THR* 3.8 5.9 - - - -
83A ALA* 2.9 31.7 + - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.8 24.1 - - + +
73A GLN* 3.5 36.1 - - + +
74A ALA* 3.7 10.3 - - + +
76A ASP 3.0 7.6 + - - +
77A PRO 3.2 7.4 + - - +
79A ALA* 1.3 75.9 - - - +
81A MSE 1.3 63.6 + - + +
83A ALA* 3.3 3.9 + - - +
84A TYR* 2.9 28.2 + - - +
127A LEU* 4.9 8.1 - - + +
128A LEU* 4.4 8.1 - - + -
131A SER* 3.6 31.0 - - - +
204A CL 4.5 0.2 - - + -
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Residues in contact with MSE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 3.0 25.0 + - + +
78A LEU* 3.7 9.6 - - + +
80A VAL* 1.3 84.3 - - + +
82A THR* 1.3 57.2 + - - +
84A TYR* 3.5 5.7 + - - +
85A LEU* 3.1 35.3 + - + +
128A LEU* 3.7 20.9 - - + +
131A SER* 3.3 37.9 - - - +
132A ILE* 3.8 16.2 - - + +
141A PHE* 5.3 6.3 - - + -
154A LEU* 3.6 30.1 - - + -
187A VAL* 5.5 5.6 - - + -
190A PHE* 4.0 22.7 - - + -
191A THR* 5.7 5.6 - - + -
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 2.9 32.0 + - - +
79A ALA* 3.8 7.6 - - - -
81A MSE 1.3 74.1 - - - +
83A ALA* 1.3 59.0 + - - +
85A LEU* 3.2 5.2 + - - +
86A ARG* 3.0 55.6 + - - +
183A ILE* 4.1 12.8 - - + +
187A VAL* 3.6 16.6 - - + +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ASP* 3.5 28.7 - - + +
70A ILE* 4.1 8.7 - - - +
73A GLN* 4.1 7.9 - - + -
79A ALA 2.9 18.3 + - - +
80A VAL 3.7 2.9 - - - +
82A THR* 1.3 72.2 - - - +
84A TYR* 1.3 60.4 + - - +
86A ARG* 3.4 11.1 + - - +
87A TRP* 2.9 32.7 + - - +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 3.8 17.8 - - + +
80A VAL 2.9 18.0 + - - +
81A MSE 3.6 3.4 - - - +
83A ALA* 1.3 76.8 - - - +
85A LEU* 1.3 62.0 + - + +
87A TRP* 3.6 10.7 - + - +
88A THR* 2.9 53.4 + - - -
124A VAL* 3.6 25.8 - - + -
128A LEU* 3.6 30.1 - - + -
154A LEU* 3.9 24.5 - - + -
155A ALA* 3.4 18.2 - - + +
158A VAL* 3.8 16.1 - - + +
159A ASN* 3.3 14.6 + - - -
209A ACY 2.6 26.9 + - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A MSE 3.1 18.4 + - + +
82A THR 3.2 6.0 + - - +
84A TYR* 1.3 79.7 - - + +
86A ARG* 1.3 57.8 + - - +
88A THR* 3.3 3.1 + - - -
89A ILE* 2.9 38.4 + - + +
154A LEU* 3.8 27.8 - - + -
158A VAL* 3.6 35.6 - - + +
183A ILE* 4.1 19.3 - - + +
186A TYR* 4.2 11.0 - - + -
187A VAL* 3.7 41.1 - - + +
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A THR* 3.0 48.4 + - - +
83A ALA* 3.8 8.9 - - - +
85A LEU* 1.3 77.4 - - - +
87A TRP* 1.3 58.8 + - - +
89A ILE* 3.5 3.0 + - - +
90A GLN* 3.0 31.1 + - + +
180A GLU* 2.9 39.2 + - - +
183A ILE* 3.8 20.7 - - + +
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Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A CYS* 3.5 28.2 + - - +
64A PHE* 4.0 7.9 - + - -
66A GLN 4.0 14.6 + - - -
67A LEU* 3.5 20.4 - - + -
69A ASP* 5.1 17.0 - - + -
70A ILE* 3.7 26.0 - - + -
83A ALA 2.9 18.6 + - - +
84A TYR* 3.6 9.2 - + - +
86A ARG* 1.3 77.2 - - - +
88A THR* 1.3 70.1 + - - +
90A GLN* 3.3 8.8 + - + +
91A ARG* 2.9 84.7 + - + +
124A VAL* 3.9 22.0 - - + -
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR* 2.9 40.8 + - - -
85A LEU 3.3 4.0 + - - -
87A TRP* 1.3 74.5 - - - +
89A ILE* 1.3 65.4 + - - +
91A ARG* 3.2 28.0 + - - +
92A HIS* 3.1 47.3 + - + +
158A VAL* 3.8 29.2 - - + -
159A ASN* 3.9 7.4 - - - +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 2.9 18.3 + - + +
86A ARG* 3.8 4.0 - - - +
88A THR* 1.3 76.4 - - - +
90A GLN* 1.3 63.1 + - - +
92A HIS* 3.1 4.5 + - - +
93A ARG* 2.9 24.0 + - + +
158A VAL* 3.9 10.3 - - + -
162A PHE* 3.8 29.8 - - + -
179A ASP* 3.3 44.2 - - + +
182A LEU* 4.2 16.4 - - + -
183A ILE* 3.5 34.5 - - + +
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 3.0 21.6 + - + +
87A TRP* 3.5 9.9 - - + +
88A THR 3.3 0.2 - - - -
89A ILE* 1.3 76.5 - - - +
91A ARG* 1.3 57.7 + - + +
93A ARG* 3.1 8.9 + - - +
94A ASN* 2.6 74.6 + - - +
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A CYS* 4.3 20.4 - - + -
64A PHE* 3.5 20.1 - - - -
87A TRP* 2.9 63.7 + - + +
88A THR* 3.2 31.5 + - - +
90A GLN* 1.3 76.7 - - + +
92A HIS* 1.3 67.8 + - - +
94A ASN* 3.5 5.8 + - - +
95A ASN* 2.9 32.6 + - - +
98A LEU* 3.3 34.6 - - + +
102A TYR* 5.3 1.4 - - - -
159A ASN* 4.7 1.0 + - - -
209A ACY 2.9 32.3 + - - -
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A THR* 3.1 30.9 + - + +
89A ILE 3.7 4.9 - - - +
91A ARG* 1.3 79.3 + - - +
93A ARG* 1.3 65.6 + - - +
95A ASN 3.4 20.9 + - - -
96A PRO* 3.6 6.8 - - - +
98A LEU* 4.5 23.7 - - + +
99A LEU* 3.6 35.0 + - + +
102A TYR* 6.1 1.6 - + - -
159A ASN* 2.9 30.0 + - - -
162A PHE* 3.7 43.4 - + + -
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 2.9 23.0 + - + +
90A GLN* 3.1 13.2 + - - +
92A HIS* 1.3 77.0 - - - +
94A ASN* 1.3 64.0 + - - +
95A ASN 3.5 0.3 + - - -
96A PRO* 4.1 9.2 - - - +
161A PHE* 4.9 3.0 - - - -
162A PHE* 3.7 26.1 - - + -
174A HIS* 2.9 33.1 + - - +
175A SER 3.7 0.8 + - - -
176A PRO* 3.7 27.7 - - + +
179A ASP* 2.8 44.0 + - - +
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Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLN* 2.6 51.9 + - - +
91A ARG* 4.0 5.6 - - - +
93A ARG* 1.3 79.7 - - - +
95A ASN* 1.3 60.2 + - + +
96A PRO* 3.7 5.5 - - - +
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Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 2.5 43.8 + - - +
91A ARG 2.9 15.2 + - - +
92A HIS* 3.4 11.3 + - - +
93A ARG 3.3 0.4 - - - -
94A ASN* 1.3 80.3 - - + +
96A PRO* 1.3 64.9 - - - +
97A GLN* 2.9 22.9 + - - +
98A LEU* 3.0 31.6 + - + +
99A LEU 4.8 0.3 + - - -
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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