Contacts of the helix formed by residues 70 - 84 (chain A) in PDB entry 3V5I
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 SER 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ILE* 2.9 14.2 + - - +
37A ASP* 4.4 6.5 - - - -
38A ASP* 4.4 3.7 + - - -
69A GLY* 1.3 70.1 - - - +
71A VAL* 1.3 59.3 + - - +
72A THR* 3.5 9.7 + - - -
73A ALA* 3.2 29.7 + - - +
74A GLY* 2.9 25.6 + - - -
99A MET* 3.9 3.1 - - - +
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Residues in contact with VAL 71 (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 GLY 3.4 5.4 + - - +
70A SER* 1.3 72.0 + - - +
72A THR* 1.3 62.9 + - + +
74A GLY* 3.2 2.9 + - - -
75A PHE* 3.0 47.0 + - + -
99A MET* 3.5 29.2 - - + +
125A PRO* 4.4 16.6 - - + -
126A LEU 6.1 0.7 - - - +
146A THR* 3.6 27.8 - - + -
150A LEU* 4.3 10.1 - - + -
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 4.6 5.0 + - - -
70A SER* 3.5 8.9 + - - -
71A VAL* 1.3 78.4 - - + +
73A ALA* 1.3 67.2 + - - +
75A PHE* 3.0 9.1 + - + +
76A ALA 3.0 19.2 + - - -
142A HIS* 6.0 1.8 - - + -
65B ASN* 4.7 2.1 + - - -
94B GLY* 3.4 17.3 - - - +
95B MET* 3.7 38.5 - - + +
119B GLU* 4.0 21.5 - - - +
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Residues in contact with ALA 73 (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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36A ILE* 3.9 8.5 - - + -
37A ASP 3.6 26.0 - - - +
38A ASP* 3.6 18.4 - - - +
41A ALA* 3.5 17.9 - - + +
70A SER* 3.2 20.7 + - - +
72A THR* 1.3 80.7 + - - +
74A GLY* 1.3 62.3 + - - +
76A ALA* 3.3 8.8 + - - +
77A ILE* 3.3 10.0 + - - +
65B ASN* 4.4 4.9 - - - +
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Residues in contact with GLY 74 (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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36A ILE* 3.8 8.7 - - - +
70A SER 2.9 11.5 + - - -
71A VAL 3.6 4.5 - - - -
72A THR 3.2 0.2 - - - -
73A ALA* 1.3 74.5 - - - +
75A PHE* 1.3 58.7 + - - +
77A ILE* 3.1 9.8 + - - +
78A TYR* 2.8 23.7 + - - +
99A MET* 3.7 25.6 - - - -
102A PHE* 5.8 0.2 - - - -
103A LEU* 3.5 12.6 - - - +
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.0 43.3 + - + -
72A THR* 3.0 11.6 + - + +
74A GLY* 1.3 73.6 - - - +
76A ALA* 1.3 64.7 + - - +
78A TYR* 4.0 14.6 - + + -
79A ASP* 2.8 29.2 + - - +
99A MET* 5.2 1.3 - - - -
102A PHE* 3.6 22.9 - + - -
146A THR* 5.1 1.1 - - + -
149A LYS* 3.5 37.2 - - + -
150A LEU* 3.6 26.2 - - + -
153A ILE* 3.8 16.8 - - + -
94B GLY* 4.5 7.2 - - - +
117B ASN* 3.8 28.0 - - + +
119B GLU* 6.5 0.4 - - - -
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Residues in contact with ALA 76 (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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41A ALA* 4.5 3.6 - - + -
45A VAL* 4.0 7.6 - - + -
72A THR 3.0 7.7 + - - +
73A ALA 3.3 9.2 + - - +
75A PHE* 1.3 75.4 - - - +
77A ILE* 1.3 61.6 + - - +
79A ASP* 4.2 1.8 - - - +
80A THR* 2.9 30.1 + - - -
65B ASN* 4.0 14.4 - - - +
93B ILE* 4.0 21.2 - - + +
94B GLY* 3.7 28.1 - - - +
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Residues in contact with ILE 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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32A LEU* 5.0 4.0 - - + -
36A ILE* 4.4 14.1 - - + -
40A VAL* 5.0 0.9 - - + -
41A ALA* 4.0 23.3 - - + +
44A ILE* 3.9 42.6 - - + -
45A VAL* 4.2 6.1 - - + -
48A LEU* 4.7 1.3 - - + -
62A LEU* 4.9 3.1 - - + -
73A ALA 3.3 10.5 + - - +
74A GLY 3.1 7.7 + - - +
76A ALA* 1.3 76.3 - - - +
78A TYR* 1.3 64.1 + - - +
80A THR* 3.0 5.6 + - - -
81A ILE* 2.9 42.7 + - + +
103A LEU* 3.9 27.8 - - + -
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Residues in contact with TYR 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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74A GLY 2.8 18.8 + - - +
75A PHE* 3.2 16.4 + + + +
77A ILE* 1.3 72.4 - - - +
79A ASP* 1.3 81.5 + - - +
81A ILE* 3.1 10.4 + - - +
82A GLN* 3.0 44.0 + - + +
102A PHE* 3.6 18.6 - + + -
103A LEU* 3.8 10.3 - - + +
106A ALA* 3.3 34.1 - - + -
153A ILE* 3.2 29.0 - - + +
156A GLU* 5.2 1.9 + - - -
157A ARG* 3.2 26.7 + - - -
117B ASN* 3.8 13.7 - - - -
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Residues in contact with ASP 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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75A PHE 2.8 21.3 + - - +
76A ALA* 4.2 2.2 - - - +
78A TYR* 1.3 85.1 - - - +
80A THR* 1.3 56.7 + - - +
82A GLN* 3.3 6.5 + - - +
83A HIS* 2.9 30.7 + - - +
93B ILE* 5.7 0.4 - - + -
94B GLY 5.7 1.5 + - - +
115B LEU* 3.2 33.1 - - + +
116B PRO* 3.8 9.3 - - + +
117B ASN* 2.7 54.5 + - - +
118B ALA* 3.5 4.0 + - - +
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Residues in contact with THR 80 (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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45A VAL* 3.7 30.8 - - + +
48A LEU* 3.8 28.9 - - + -
49A LEU* 4.5 9.0 - - + -
76A ALA 2.9 18.8 + - - -
77A ILE 3.0 5.5 + - - -
79A ASP* 1.3 74.5 - - - +
81A ILE* 1.3 66.1 + - - +
83A HIS* 3.0 15.7 + - + +
84A ILE* 3.1 23.6 + - + +
63B TYR* 6.1 0.5 - - - -
93B ILE* 4.4 5.4 - - - +
115B LEU* 4.4 9.1 - - - +
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Residues in contact with ILE 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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48A LEU* 3.8 17.7 - - + -
62A LEU* 4.1 19.1 - - + -
77A ILE* 2.9 39.0 + - + +
78A TYR* 3.5 10.1 - - - +
80A THR* 1.3 74.3 - - - +
82A GLN* 1.3 69.9 + - - +
83A HIS 3.3 0.2 + - - -
84A ILE* 3.3 22.3 + - - +
86A PRO 4.8 1.7 - - - +
88A VAL* 3.8 33.2 - - + +
90A THR* 5.3 1.6 - - + -
103A LEU* 4.8 10.3 - - + +
106A ALA* 3.8 28.3 - - + +
107A GLY* 5.1 0.4 - - - -
108A ALA 5.5 1.3 - - - +
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Residues in contact with GLN 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 TYR* 3.0 55.3 + - + +
79A ASP* 3.8 7.9 - - - +
81A ILE* 1.3 82.2 + - - +
83A HIS* 1.3 60.2 + - - +
84A ILE 3.6 4.5 + - - +
106A ALA* 3.1 25.0 + - - +
107A GLY 6.0 0.4 - - - -
157A ARG* 3.6 21.5 + - - +
192B PRO* 4.0 29.6 - - + +
193B GLU 4.4 5.4 + - - -
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Residues in contact with HIS 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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49A LEU* 5.3 6.5 - - + +
52A GLN* 4.6 4.6 + - - -
79A ASP 2.9 17.6 + - - +
80A THR* 3.0 9.5 + - - +
82A GLN* 1.3 79.4 - - - +
84A ILE* 1.3 69.8 + - - +
63B TYR* 5.3 7.0 - + - -
115B LEU* 4.3 13.6 - - + +
116B PRO* 6.5 0.7 - - + -
190B MET* 3.3 45.2 - - + +
191B VAL 4.8 10.8 - - - -
192B PRO* 4.9 4.0 - - + -
193B GLU* 4.0 32.7 + - + +
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Residues in contact with ILE 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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48A LEU* 4.1 20.6 - - + +
49A LEU* 4.2 18.8 - - + -
52A GLN* 3.3 30.3 - - + +
60A ILE* 3.8 28.9 - - + -
80A THR* 3.1 16.4 + - + +
81A ILE 3.3 20.7 - - - +
82A GLN 3.8 4.7 - - - +
83A HIS* 1.3 85.5 - - - +
85A LYS* 1.3 64.0 + - - +
86A PRO* 3.9 14.0 - - + +
88A VAL* 3.9 15.7 - - + -
193B GLU* 5.7 3.5 - - - -
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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