Contacts of the helix formed by residues 68 - 90 (chain A) in PDB entry 5DIR
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 TRP 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 3.1 32.1 - - + -
60A SER* 4.6 2.2 - - - +
62A LEU* 4.1 16.8 - - + -
63A ALA* 3.3 26.1 - - + +
65A SER* 2.7 42.1 + - - -
66A SER* 3.5 3.0 + - - -
67A GLY* 1.3 75.1 - - - +
69A GLN* 1.3 106.6 + - + +
70A ARG 3.1 2.5 - - - -
71A TRP* 3.0 11.4 + - - +
72A LEU* 2.8 59.9 + - + +
73A PHE* 4.3 5.8 - + - -
205E 5BV 4.7 1.3 - - + -
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.5 19.4 - - - +
56A GLY 3.0 27.1 + - - +
57A ALA* 4.9 0.6 - - - +
59A PHE* 5.1 1.1 - - + -
60A SER* 4.2 13.9 - - - +
65A SER 5.0 0.2 + - - -
66A SER* 4.9 6.7 + - - +
67A GLY* 3.2 22.9 + - - +
68A TRP* 1.3 120.7 + - + +
70A ARG* 1.3 62.1 + - - +
72A LEU 4.5 0.2 - - - +
73A PHE* 3.1 58.5 + - + +
116A ARG* 4.1 1.4 - - - -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR 5.0 1.2 + - - -
67A GLY* 3.5 15.3 + - - +
68A TRP 3.1 0.6 - - - -
69A GLN* 1.3 80.7 - - - +
71A TRP* 1.3 93.8 + - + +
74A ALA* 3.2 23.0 + - - +
116A ARG* 2.9 39.7 + - + +
117A MET* 2.8 26.1 + - + +
118A VAL 4.5 3.0 + - - -
119A LEU 3.8 8.3 + - - -
120A GLY* 4.1 27.6 - - - +
206A OLC 3.3 37.2 + - - -
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Residues in contact with TRP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY 3.5 20.4 + - - -
68A TRP* 3.0 9.5 + - - +
70A ARG* 1.3 118.5 - - + +
72A LEU* 1.3 60.8 + - - +
73A PHE 3.3 1.1 - - - -
74A ALA* 3.6 2.5 - - - +
75A LEU* 2.8 30.5 + - - +
117A MET* 3.4 35.9 - - + -
206A OLC 4.3 25.6 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TRP* 2.8 50.4 + - + +
71A TRP* 1.3 74.2 - - - +
73A PHE* 1.3 61.2 + - + +
75A LEU* 3.2 19.5 + - + +
76A ILE* 2.9 46.7 + - + +
205E 5BV 3.7 24.2 - - + -
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY* 4.9 3.1 - - - -
59A PHE* 3.9 30.7 - + + -
68A TRP* 4.3 3.1 - + - -
69A GLN* 3.1 46.6 + - + +
72A LEU* 1.3 81.8 - - + +
74A ALA* 1.3 60.1 + - - +
76A ILE* 3.9 12.8 - - + -
77A ALA* 2.9 28.1 + - - +
116A ARG* 3.5 25.2 + - - +
201E MLE 3.6 9.9 - - - -
204E ALO 4.0 6.7 - - - -
205E 5BV 3.4 63.0 - - + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG 3.2 22.4 + - - +
71A TRP 3.4 4.7 + - - +
73A PHE* 1.3 77.4 - - - +
75A LEU* 1.3 58.3 + - - +
77A ALA* 3.2 3.4 + - - +
78A ILE* 2.9 37.4 + - + +
113A LEU* 3.5 18.3 - - + +
116A ARG* 4.1 8.9 - - + +
117A MET* 3.4 26.7 - - + -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TRP 2.8 18.4 + - - +
72A LEU* 3.3 19.1 - - + +
73A PHE 3.2 0.2 - - - -
74A ALA* 1.3 77.1 - - - +
76A ILE* 1.3 57.8 + - + +
78A ILE* 3.2 17.0 + - + +
79A VAL* 3.0 45.7 + - + +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 2.9 36.3 + - + +
73A PHE* 3.8 27.6 - - + +
74A ALA 3.3 0.2 - - - -
75A LEU* 1.3 77.0 - - + +
77A ALA* 1.3 58.9 + - - +
79A VAL* 3.8 5.7 - - - +
80A VAL* 2.8 44.7 + - + +
201E MLE 4.1 13.9 - - + -
205E 5BV 4.2 29.4 - - + -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE 2.9 17.9 + - - +
74A ALA* 3.2 6.5 + - - +
76A ILE* 1.3 77.0 - - - +
78A ILE* 1.3 50.8 + - - +
80A VAL* 3.8 0.7 - - - +
81A SER* 2.7 43.7 + - - +
109A ALA* 4.2 9.0 - - + +
113A LEU* 4.0 27.8 - - + +
116A ARG* 5.6 2.0 - - - +
201E MLE 3.9 22.5 - - + +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 2.9 27.5 + - + +
75A LEU* 3.2 17.7 + - + +
77A ALA* 1.3 75.8 - - - +
79A VAL* 1.3 66.1 + - + +
81A SER* 3.6 5.3 - - - -
82A ALA* 3.1 24.5 + - + +
113A LEU* 3.9 23.8 - - + -
117A MET* 5.3 7.9 - - - -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.0 35.8 + - + +
76A ILE* 3.8 5.6 - - - +
78A ILE* 1.3 79.9 - - + +
80A VAL* 1.3 68.7 + - + +
82A ALA* 3.4 6.5 + - - +
83A SER* 3.3 21.6 + - - +
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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
----------------------------------------------------------
76A ILE* 2.8 40.1 + - + +
79A VAL* 1.3 76.4 - - + +
81A SER* 1.3 62.4 + - - +
83A SER* 2.9 23.3 + - - +
84A LEU* 2.9 30.2 + - + +
105A VAL* 5.6 0.2 - - + -
109A ALA* 5.8 1.3 - - + -
201E MLE 3.9 29.2 - - + -
205E 5BV 6.1 0.7 - - + -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 2.7 25.7 + - - -
78A ILE* 3.6 7.0 - - - -
80A VAL* 1.3 78.2 - - - +
82A ALA* 1.3 62.1 + - - +
84A LEU* 3.1 5.2 + - - +
85A VAL* 2.9 28.5 + - - +
106A LEU* 3.6 22.2 - - - +
109A ALA* 3.8 12.4 - - - +
110A LEU* 3.7 24.1 - - - +
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Residues in contact with ALA 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 ILE* 3.1 11.4 + - + +
79A VAL* 3.6 10.1 - - - +
81A SER* 1.3 77.3 - - - +
83A SER* 1.3 63.4 + - - +
85A VAL* 3.1 18.6 + - - +
86A VAL* 3.2 18.4 + - + +
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.3 11.3 + - - +
80A VAL* 2.9 22.5 + - - +
82A ALA* 1.3 78.6 - - - +
84A LEU* 1.3 63.7 + - - +
86A VAL* 3.2 23.6 - - - +
87A TRP* 3.3 13.6 + - - +
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Residues in contact with LEU 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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80A VAL* 2.9 31.9 + - + +
81A SER* 3.4 6.7 - - - +
82A ALA 3.1 0.2 - - - -
83A SER* 1.3 78.7 + - - +
85A VAL* 1.3 59.1 + - - +
87A TRP* 3.4 20.0 + - + +
88A LEU* 3.0 26.2 + - - +
102A LEU* 3.6 35.2 - - + +
105A VAL* 3.6 35.9 - - + -
106A LEU* 4.2 22.0 - - + +
109A ALA* 5.7 1.3 - - + -
153A LEU* 5.6 2.5 - - + -
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Residues in contact with VAL 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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10A LEU* 6.1 0.9 - - + -
13A LEU* 5.1 17.5 - - + -
81A SER* 2.9 21.4 + - - +
82A ALA* 3.1 9.1 + - - +
84A LEU* 1.3 73.5 - - - +
86A VAL* 1.3 67.5 + - + +
88A LEU* 2.9 19.5 + - + +
89A LYS* 3.0 28.2 + - + +
106A LEU* 3.7 26.5 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 3.2 9.1 + - - +
83A SER* 3.2 22.7 - - - +
85A VAL* 1.3 77.1 - - + +
87A TRP* 1.3 62.6 + - + +
89A LYS* 3.1 17.6 + - + +
90A ARG* 3.0 41.0 + - + +
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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
----------------------------------------------------------
83A SER 3.3 14.5 + - - +
84A LEU* 3.7 19.1 - - + +
85A VAL 3.1 0.8 - - - -
86A VAL* 1.3 79.4 - - + +
88A LEU* 1.3 63.8 + - - +
90A ARG* 3.7 36.4 + - + +
91A LEU* 3.2 28.6 + - + +
98A LEU* 4.6 14.8 - - + +
102A LEU* 3.5 30.1 - - + -
153A LEU* 3.9 34.5 - - + -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.3 30.2 - - + +
10A LEU* 5.2 1.1 - - + -
12A TRP* 4.1 11.2 - - + -
13A LEU* 3.6 33.4 - - + -
84A LEU 3.0 12.7 + - - +
85A VAL* 2.9 12.2 + - + +
87A TRP* 1.3 76.1 - - - +
89A LYS* 1.3 65.5 + - + +
91A LEU* 3.2 21.0 + - + +
99A ALA* 3.7 42.6 - - + +
102A LEU* 3.8 18.6 - - + +
103A ALA* 5.4 4.0 - - + +
106A LEU* 5.9 0.7 - - + -
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Residues in contact with LYS 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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9A ARG* 3.8 12.6 + - - +
10A LEU* 3.6 31.4 - - + -
85A VAL* 3.0 30.6 + - + +
86A VAL* 3.4 17.3 - - + +
88A LEU* 1.3 75.2 - - + +
90A ARG* 1.3 59.3 + - + +
91A LEU 3.0 17.2 + - - +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.0 24.8 + - + +
87A TRP* 3.8 38.6 - - + +
88A LEU 3.3 0.8 - - - -
89A LYS* 1.3 75.4 - - + +
91A LEU* 1.3 63.4 + - - +
92A LYS* 4.0 5.5 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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