Contacts of the helix formed by residues 74 - 93 (chain D) in PDB entry 2VT4
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 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D GLN 5.5 0.2 - - - +
71D ARG 4.5 8.7 - - - +
72D LEU 3.4 6.8 + - - -
73D GLN* 1.3 85.9 - - - +
75D LEU* 1.3 65.9 + - - +
76D THR* 3.9 7.4 + - - -
77D ASN* 3.0 35.0 + - - +
78D LEU* 3.3 12.4 + - - +
155D ARG* 3.9 10.3 - - - +
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Residues in contact with LEU 75 (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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74D THR* 1.3 71.8 - - - +
76D THR* 1.3 67.0 + - - +
78D LEU* 3.0 25.1 + - + +
79D PHE* 3.5 13.9 + - + -
138D ASP* 4.9 3.1 - - - +
139D ARG* 5.4 1.3 - - - +
149D TYR* 3.0 36.6 - - + +
150D GLN* 5.8 1.3 - - - +
153D MET* 3.2 27.6 - - + +
154D THR* 3.4 33.2 - - - +
155D ARG* 3.9 20.3 - - + +
158D ALA* 4.2 8.9 - - + +
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D THR* 3.3 7.9 + - - -
75D LEU* 1.3 77.8 - - - +
77D ASN* 1.3 65.2 + - - +
79D PHE* 3.1 24.7 + - - +
80D ILE* 3.1 17.2 + - + +
135D ILE* 4.8 9.2 - - + -
138D ASP* 3.4 4.1 + - - +
139D ARG* 3.1 34.9 + - - -
292D LEU* 4.1 32.8 - - + -
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Residues in contact with ASN 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ILE* 3.5 20.8 - - + +
72D LEU* 2.6 51.5 + - - +
74D THR* 3.0 22.5 + - - +
76D THR* 1.3 77.6 - - - +
78D LEU* 1.3 54.6 + - - +
79D PHE 3.3 0.2 - - - -
80D ILE* 3.3 19.6 - - - +
81D THR* 2.8 35.7 + - - -
349D PHE* 4.3 11.2 - - - -
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ILE* 5.2 2.9 - - + +
74D THR 3.3 10.4 + - - +
75D LEU* 3.0 15.3 + - + +
77D ASN* 1.3 75.7 - - - +
79D PHE* 1.3 63.9 + - + +
81D THR* 3.1 22.0 + - + +
82D SER 3.2 8.7 + - - -
155D ARG* 4.0 41.5 - - + +
158D ALA* 4.1 21.8 - - + -
159D LYS* 4.5 22.0 - - + -
162D ILE* 3.6 20.4 - - + +
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Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 3.9 14.8 - - + -
76D THR* 3.1 9.3 + - - +
78D LEU* 1.3 74.9 - - - +
80D ILE* 1.3 64.9 + - - +
82D SER* 3.0 9.3 + - - -
83D LEU* 3.0 21.5 + - - +
131D THR* 3.5 9.3 - - + +
134D VAL* 3.8 24.9 - - + -
135D ILE* 3.4 32.3 - - + -
138D ASP* 3.6 39.7 - - + -
153D MET* 4.9 4.9 - - + -
158D ALA* 4.0 40.2 - - + -
161D ILE* 4.6 11.9 - - + -
162D ILE* 4.0 15.0 - - + -
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Residues in contact with ILE 80 (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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62D VAL* 4.0 10.5 - - + -
66D ILE* 3.7 19.1 - - + -
76D THR* 3.1 16.7 + - + +
77D ASN* 3.3 23.8 - - - +
78D LEU 3.3 0.2 - - - -
79D PHE* 1.3 75.1 - - - +
81D THR* 1.3 58.3 + - - +
83D LEU* 3.2 12.3 - - + +
84D ALA* 3.0 24.8 + - + +
135D ILE* 4.3 13.2 - - + -
292D LEU* 4.2 22.7 - - + -
295D ILE* 5.8 2.5 - - + -
343D TYR* 3.4 40.1 + - + +
349D PHE* 5.0 3.1 - - + -
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Residues in contact with THR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ILE* 4.0 23.3 - - + +
66D ILE* 3.5 21.8 - - - +
77D ASN 2.8 19.8 + - - -
78D LEU* 3.2 17.1 - - + +
79D PHE 3.1 0.2 - - - -
80D ILE* 1.3 74.2 - - - +
82D SER* 1.3 64.8 + - - +
83D LEU 3.1 0.4 - - - -
84D ALA* 3.4 7.6 + - - +
85D CYS* 3.2 28.3 + - - -
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Residues in contact with SER 82 (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 LEU 3.2 9.8 + - - -
79D PHE* 3.0 11.3 + - - -
81D THR* 1.3 78.4 - - - +
83D LEU* 1.3 62.8 + - - +
85D CYS* 3.1 17.4 + - - +
86D ALA* 3.2 11.1 + - - +
131D THR* 3.8 16.2 + - - -
162D ILE* 3.6 29.2 - - - +
166D TRP* 3.0 33.9 + - - +
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Residues in contact with LEU 83 (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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79D PHE 3.0 9.8 + - - +
80D ILE* 3.2 16.2 - - + +
82D SER* 1.3 77.9 - - - +
84D ALA* 1.3 56.5 + - - +
86D ALA* 3.6 5.2 - - + +
87D ASP* 3.4 25.8 + - - +
128D SER* 3.8 41.3 - - - +
131D THR* 4.3 7.4 - - + +
132D LEU* 3.5 31.9 - - + -
135D ILE* 4.1 15.0 - - + -
295D ILE* 4.6 2.2 - - + -
299D PHE* 6.4 0.2 - - + -
339D ASN* 4.3 22.2 - - - +
343D TYR* 4.9 5.4 - - - +
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Residues in contact with ALA 84 (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 ASN* 3.5 31.9 - - + +
62D VAL* 4.4 11.2 - - + -
63D ILE* 4.2 19.8 - - + +
80D ILE 3.0 14.0 + - - +
81D THR* 3.8 7.6 - - - +
82D SER 3.2 0.6 - - - -
83D LEU* 1.3 74.3 - - - +
85D CYS* 1.3 61.7 + - - +
87D ASP* 3.4 3.3 + - - +
88D LEU* 2.8 26.9 + - - +
343D TYR* 6.4 0.2 - - + -
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Residues in contact with CYS 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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63D ILE* 4.0 17.5 - - - -
81D THR* 3.2 25.1 - - - -
82D SER* 3.1 10.8 + - - +
84D ALA* 1.3 74.2 - - - +
86D ALA* 1.3 68.2 + - - +
87D ASP 3.0 0.9 - - - -
88D LEU* 3.5 8.1 - - + +
89D VAL* 2.8 33.0 + - + +
166D TRP* 4.5 9.2 - - + -
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Residues in contact with ALA 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 SER 3.2 12.2 + - - +
83D LEU* 3.6 13.5 - - + +
85D CYS* 1.3 75.4 - - - +
87D ASP* 1.3 59.0 + - - +
89D VAL 3.4 0.5 + - - -
90D VAL* 3.1 31.2 + - - +
124D CYS* 3.5 16.5 - - + +
127D ALA* 4.9 0.7 - - + -
128D SER* 3.6 27.6 - - - +
166D TRP* 3.8 23.8 - - + -
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Residues in contact with ASP 87 (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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55D ILE* 3.2 12.0 - - - +
59D ASN* 3.6 28.8 - - - +
83D LEU* 3.4 16.4 + - - +
84D ALA 3.7 2.2 - - - +
85D CYS 3.0 0.6 - - - -
86D ALA* 1.3 80.5 - - - +
88D LEU* 1.3 65.1 + - - +
89D VAL 3.2 0.2 - - - -
90D VAL* 3.2 3.3 + - - +
91D GLY 2.9 19.1 + - - -
128D SER* 4.4 9.4 + - - -
335D ASN* 4.4 7.1 + - - +
336D SER* 2.8 44.2 + - - +
339D ASN* 4.6 13.9 + - - +
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Residues in contact with LEU 88 (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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55D ILE* 5.0 1.1 - - - -
56D VAL* 3.9 34.8 - - + +
59D ASN* 4.6 6.8 - - + +
60D VAL* 4.0 19.7 - - + +
63D ILE* 4.3 20.2 - - + -
84D ALA 2.8 19.1 + - - +
85D CYS* 3.2 10.7 + - - +
87D ASP* 1.3 72.1 - - - +
89D VAL* 1.3 64.5 + - + +
91D GLY* 3.1 1.9 + - - -
92D LEU* 3.0 49.8 + - + +
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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 CYS* 2.8 22.3 + - + +
86D ALA* 3.7 5.6 - - - +
88D LEU* 1.3 78.7 - - + +
90D VAL* 1.3 62.4 + - - +
92D LEU* 4.9 2.5 - - - -
93D LEU* 2.9 45.2 + - + +
94D VAL* 3.5 5.2 + - + -
120D LEU* 4.8 16.6 - - + -
123D LEU* 5.8 2.2 - - + -
124D CYS* 3.5 20.9 - - - -
166D TRP* 5.4 6.7 - - + -
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Residues in contact with VAL 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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55D ILE* 4.8 1.6 - - + -
86D ALA 3.1 19.1 + - - +
87D ASP* 3.2 7.4 + - - +
89D VAL* 1.3 76.4 - - - +
91D GLY* 1.3 58.2 + - - +
92D LEU 3.6 0.2 + - - -
94D VAL* 3.9 14.4 - - + -
95D VAL* 2.9 48.6 + - + +
124D CYS* 3.6 23.6 - - + -
125D VAL* 6.5 0.2 - - + -
128D SER* 6.1 0.4 - - - +
333D TYR* 4.1 20.0 - - + +
336D SER* 3.6 25.8 - - - +
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Residues in contact with GLY 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 VAL* 3.8 13.4 - - - +
55D ILE* 3.7 28.2 - - - +
56D VAL* 3.7 16.3 - - - +
87D ASP 2.9 10.5 + - - -
88D LEU 3.1 4.5 + - - -
90D VAL* 1.3 77.9 - - - +
92D LEU* 1.3 57.8 + - - +
95D VAL* 4.8 1.8 - - - -
96D PRO* 3.3 18.2 - - - +
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Residues in contact with LEU 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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52D VAL* 6.0 1.3 - - + -
56D VAL* 3.8 26.0 - - + -
88D LEU* 3.0 39.5 + - + +
89D VAL* 4.4 1.1 - - - +
91D GLY* 1.3 78.6 - - - +
93D LEU* 1.3 76.0 + - + +
96D PRO* 3.3 17.2 - - - +
97D PHE* 4.8 3.8 - - - -
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Residues in contact with LEU 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 30.4 + - + +
92D LEU* 1.3 94.5 - - + +
94D VAL* 1.3 66.7 + - - +
96D PRO* 3.9 0.9 - - - -
97D PHE* 3.1 40.6 + - + +
117D TRP* 4.0 4.7 - - - -
120D LEU* 4.3 27.6 - - + -
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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