Contacts of the helix formed by residues 82 - 99 (chain D) in PDB entry 2VE7
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 PHE 82 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU* 4.2 5.8 - - + -
158B LEU* 3.3 33.1 + - + +
159B GLY* 4.3 1.0 + - - -
187B TRP* 4.3 4.9 - - + -
191B CYS* 3.4 62.6 - - + -
194B ILE* 3.9 21.1 - - + -
195B HIS* 4.1 11.9 - - + -
79D MET* 3.0 10.2 + - + +
81D GLY* 1.3 78.0 - - - +
83D LEU* 1.3 65.4 + - - +
84D PRO 3.4 0.9 - - - -
85D PHE* 3.0 50.9 + + - +
86D SER* 3.1 25.8 + - - -
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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
----------------------------------------------------------
194B ILE* 3.9 32.3 - - + -
198B MET* 5.2 1.1 - - + -
64D PHE 3.2 9.0 - - - +
65D TYR* 3.4 25.6 - - + +
66D MET 3.7 18.6 - - - +
67D MET* 4.2 31.9 - - + -
68D PRO* 4.9 0.2 - - + -
76D PRO 5.7 0.4 - - - +
79D MET 3.3 10.6 + - - +
80D GLU* 4.0 22.2 - - + +
82D PHE* 1.3 77.2 - - + +
84D PRO* 1.3 70.2 - - + +
86D SER* 3.1 4.2 + - - -
87D ASN* 3.0 27.8 + - - +
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Residues in contact with PRO 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D HIS* 3.8 18.8 + - + +
50D MET* 4.8 5.4 - - + -
64D PHE* 3.0 29.5 - - + +
65D TYR* 3.9 21.1 - - + +
80D GLU 3.1 20.9 - - - +
81D GLY* 3.5 13.0 - - - +
82D PHE 3.6 0.7 - - - -
83D LEU* 1.3 88.1 - - + +
85D PHE* 1.3 57.2 + - - +
87D ASN* 4.1 0.2 - - - +
88D LEU* 2.8 34.3 + - - +
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.9 7.9 - - + -
157B ASP 5.2 7.4 - - - +
158B LEU* 4.6 4.9 - - + +
195B HIS* 4.7 5.8 - + - -
46D HIS* 4.0 15.1 - - + -
81D GLY 5.1 2.0 - - - +
82D PHE* 3.0 47.7 + + + +
84D PRO* 1.3 80.3 - - - +
86D SER* 1.3 69.7 + - - +
88D LEU* 3.2 2.4 + - - +
89D VAL* 2.9 39.0 + - + +
106D THR* 3.7 29.6 - - + -
109D ILE* 4.0 17.3 - - + -
110D LEU* 3.4 45.3 - - + -
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Residues in contact with SER 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 4.1 2.3 - - - +
195B HIS* 3.0 34.7 + - - -
198B MET* 3.1 24.0 - - - +
82D PHE* 3.1 29.7 + - - -
83D LEU 3.7 4.9 - - - -
85D PHE* 1.3 83.0 - - - +
87D ASN* 1.3 54.1 + - - +
89D VAL* 3.4 4.2 + - - +
90D THR* 2.8 34.9 + - - -
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Residues in contact with ASN 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B MET* 3.5 23.9 - - - +
202B SER* 4.2 9.3 + - - -
63D HIS 3.8 12.2 + - - -
64D PHE* 3.2 29.6 - - + +
66D MET* 3.4 22.8 + - - +
83D LEU 3.0 19.3 + - - +
84D PRO 4.1 2.0 - - - +
86D SER* 1.3 74.1 - - - +
88D LEU* 1.3 67.0 + - - +
90D THR* 3.0 7.4 + - - +
91D HIS* 2.9 42.4 + - + -
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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
----------------------------------------------------------
46D HIS* 4.1 34.1 - - + +
49D TYR* 4.1 20.4 - - + -
50D MET* 4.2 2.2 - - + +
53D LEU* 3.5 25.6 - - + -
64D PHE* 3.9 17.2 - - + -
84D PRO 2.8 26.1 + - - +
85D PHE* 3.4 5.8 - - - +
87D ASN* 1.3 71.9 - - - +
89D VAL* 1.3 58.2 + - - +
91D HIS* 3.9 0.7 - - - -
92D LEU* 2.9 44.4 + - + +
109D ILE* 3.8 32.3 - - + -
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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
----------------------------------------------------------
195B HIS* 3.8 17.0 - - + +
199B LYS* 5.1 3.4 - - - +
85D PHE* 2.9 37.3 + - + +
86D SER 3.5 4.7 - - - +
88D LEU* 1.3 74.7 - - - +
90D THR* 1.3 67.1 + - - +
92D LEU* 3.4 5.9 + - - +
93D ASP* 2.9 39.8 + - - +
104D PHE* 4.9 6.1 - - + -
106D THR* 3.6 36.6 - - + +
109D ILE* 4.2 16.2 - - + -
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Residues in contact with THR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B HIS* 4.9 4.5 - - - -
198B MET* 3.1 38.0 - - + +
199B LYS* 5.9 1.6 - - + +
86D SER 2.8 15.8 + - - -
87D ASN* 3.0 10.3 + - - +
89D VAL* 1.3 76.0 - - - +
91D HIS* 1.3 65.6 + - + +
93D ASP* 3.2 25.1 - - - +
94D SER* 3.8 5.5 + - - -
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Residues in contact with HIS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LEU* 3.7 25.4 - - + -
57D TYR* 5.2 4.5 - + + -
59D ILE* 4.2 26.6 - - + +
63D HIS* 4.8 8.7 - - + -
64D PHE* 3.9 16.3 - + - -
87D ASN* 2.9 44.5 + - + +
90D THR* 1.3 79.0 - - + +
92D LEU* 1.3 56.9 + - - +
93D ASP 2.9 4.9 - - - -
94D SER* 2.8 24.4 + - - +
95D PHE* 2.9 13.3 + - - +
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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
----------------------------------------------------------
49D TYR* 3.8 34.1 - - + +
53D LEU* 3.9 21.3 - - + -
88D LEU* 2.9 28.6 + - + +
89D VAL 3.4 1.1 + - - +
91D HIS* 1.3 76.8 - - - +
93D ASP* 1.3 62.1 + - - +
95D PHE* 4.3 13.0 - - + +
96D LEU* 3.1 44.2 + - + +
104D PHE* 3.5 40.3 - - + +
109D ILE* 3.6 18.4 - - + -
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Residues in contact with ASP 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS* 5.3 5.9 + - - -
89D VAL* 2.9 33.1 + - - +
90D THR* 3.2 16.0 - - - +
91D HIS 2.9 0.2 - - - -
92D LEU* 1.3 78.1 - - - +
94D SER* 1.3 56.9 + - - +
97D PRO* 3.0 24.5 - - - +
104D PHE* 4.3 15.2 - - - +
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Residues in contact with SER 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D TYR* 3.2 18.7 + - - -
90D THR 4.5 5.8 - - - -
91D HIS* 2.8 10.4 + - - -
93D ASP* 1.3 81.5 - - - +
95D PHE* 1.3 61.6 + - - +
97D PRO* 3.4 10.2 - - - +
98D ILE* 3.8 16.1 + - - +
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Residues in contact with PHE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ALA* 4.5 10.8 - - + -
53D LEU* 3.7 24.5 - - + -
56D VAL* 3.8 26.9 - - + -
57D TYR* 3.6 24.7 - + + +
91D HIS 2.9 14.1 + - - +
92D LEU* 4.3 10.1 - - + +
94D SER* 1.3 77.1 + - - +
96D LEU* 1.3 68.2 + - + +
97D PRO 3.3 0.2 - - - -
98D ILE* 2.8 33.3 + - + +
99D CYS* 3.1 32.0 + - - -
124D ILE* 3.7 26.7 - - + -
127D PHE* 3.8 26.2 - + - -
128D ILE* 5.6 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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49D TYR* 5.4 1.3 - - + -
92D LEU* 3.1 27.3 + - + +
95D PHE* 1.3 81.3 - - + +
97D PRO* 1.4 68.2 - - + +
99D CYS* 3.0 13.8 + - + +
100D ARG 3.1 0.2 + - - -
101D VAL* 2.8 44.0 + - + +
104D PHE* 3.0 49.8 - - + -
120D PHE* 4.8 11.9 - - + +
124D ILE* 3.8 35.9 - - + -
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Residues in contact with PRO 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU 3.9 0.2 - - - +
93D ASP 3.0 28.0 - - - +
94D SER* 3.4 11.4 - - - +
96D LEU* 1.4 91.6 - - + +
98D ILE* 1.3 56.6 + - + +
100D ARG* 2.9 25.3 + - - -
101D VAL 3.0 13.4 - - - +
102D ASN* 3.8 20.3 - - - +
104D PHE* 6.3 0.2 - - + -
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Residues in contact with ILE 98 (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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226B LEU* 5.5 2.9 - - + -
230B ILE* 3.7 42.4 - - + -
233B TYR* 3.5 21.2 - - + -
57D TYR* 3.3 27.1 - - + +
94D SER* 3.8 13.7 - - - +
95D PHE* 2.8 16.9 + - + +
97D PRO* 1.3 73.9 - - + +
99D CYS* 1.3 55.1 + - - +
100D ARG* 3.0 14.7 + - - +
127D PHE* 3.6 35.9 - - + -
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Residues in contact with CYS 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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233B TYR* 4.7 1.5 + - - -
95D PHE* 3.4 49.1 - - - -
96D LEU* 3.0 12.8 + - + +
98D ILE* 1.3 72.3 - - - +
100D ARG* 1.3 71.2 + - - +
101D VAL* 3.4 4.9 + - + +
123D GLY* 3.3 36.3 - - - +
124D ILE* 3.7 19.1 - - + +
127D PHE* 4.0 14.1 - - - -
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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