Contacts of the helix formed by residues 74 - 89 (chain A) in PDB entry 3IEW
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASP* 3.6 8.7 - - - +
72A GLY 3.5 2.6 + - - -
73A ALA* 1.3 71.0 - - - +
75A SER* 1.3 56.5 + - - +
76A ARG* 2.9 27.0 + - - +
77A ALA* 3.0 36.2 + - + +
78A LEU* 3.2 12.6 + - - +
80A ARG* 4.5 7.8 + - - -
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Residues in contact with SER 75 (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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37A SER* 3.8 4.3 + - - -
38A ASP* 2.5 33.4 + - - -
40A ASP* 3.7 14.8 - - - -
43A LEU* 3.8 10.9 - - - +
44A HIS* 2.6 35.2 + - - -
47A THR* 5.0 1.2 + - - -
73A ALA 3.2 1.9 + - - -
74A ASP* 1.3 70.6 - - - +
76A ARG* 1.3 57.8 + - - +
78A LEU* 3.4 12.6 + - - +
79A LEU* 2.8 28.4 + - - +
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Residues in contact with ARG 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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24A GLY* 3.9 23.4 + - - -
43A LEU* 3.4 22.0 - - + -
74A ASP* 2.9 17.0 + - - +
75A SER* 1.3 76.2 - - - +
77A ALA* 1.3 60.1 + - - +
79A LEU* 3.2 3.4 + - - +
80A ARG* 2.9 48.1 + - - +
117A ASN* 3.2 46.9 + - - +
120A ALA* 4.1 10.1 - - - +
121A ASP* 2.9 37.8 + - - +
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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
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74A ASP* 3.0 22.4 + - + +
76A ARG* 1.3 77.0 - - - +
78A LEU* 1.3 59.8 + - + +
80A ARG* 3.3 25.7 + - - +
81A GLU* 3.0 29.3 + - - +
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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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37A SER* 4.7 7.4 - - - -
44A HIS* 5.0 7.0 - - + +
47A THR* 4.8 4.9 - - + +
59A ILE* 5.4 6.3 - - + -
63A PHE* 3.6 54.3 - - + -
70A PHE* 3.9 22.9 - - + -
73A ALA* 4.1 20.0 - - + -
74A ASP 3.2 10.3 + - - +
75A SER* 3.5 21.5 - - - +
76A ARG 3.2 0.4 - - - -
77A ALA* 1.3 78.4 - - + +
79A LEU* 1.3 56.4 + - - +
81A GLU* 3.2 2.3 + - + -
82A CYS* 2.9 29.0 + - - +
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Residues in contact with LEU 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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43A LEU* 4.0 25.6 - - + +
46A ILE* 4.0 11.4 - - + -
47A THR* 3.5 24.0 + - - +
50A LEU* 3.8 17.0 - - + -
75A SER 2.8 20.7 + - - +
76A ARG* 3.6 5.2 - - - +
78A LEU* 1.3 73.3 - - - +
80A ARG* 1.3 57.8 + - - +
82A CYS* 3.2 5.0 + - - +
83A ALA* 2.9 27.9 + - - +
118A ILE* 4.5 11.2 - - + -
121A ASP* 3.8 25.6 - - + +
122A LEU* 3.8 27.6 - - + -
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Residues in contact with ARG 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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74A ASP* 4.5 7.1 + - - -
76A ARG* 2.9 37.7 + - - +
77A ALA* 3.6 27.4 - - - +
79A LEU* 1.3 77.6 - - - +
81A GLU* 1.3 60.8 + - - +
83A ALA* 3.5 2.1 + - - +
84A SER* 3.1 22.2 + - - -
120A ALA 5.6 0.2 - - - -
121A ASP* 2.9 59.6 + - + +
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Residues in contact with GLU 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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63A PHE* 3.7 15.5 - - + -
77A ALA 3.0 17.0 + - - +
78A LEU* 3.2 5.6 + - + +
80A ARG* 1.3 72.2 - - - +
82A CYS* 1.3 67.0 + - - +
84A SER* 3.2 14.4 + - - -
85A ARG* 2.8 70.8 + - - +
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Residues in contact with CYS 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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47A THR* 3.6 38.6 - - + -
50A LEU* 3.7 26.7 - - - -
51A PHE* 3.6 33.5 - - + -
63A PHE* 4.0 0.8 - - - -
78A LEU 2.9 13.8 + - - +
79A LEU* 3.4 7.9 - - - +
81A GLU* 1.3 76.5 - - - +
83A ALA* 1.3 58.4 + - - +
85A ARG* 3.1 4.6 + - - +
86A VAL* 2.9 32.6 + - - +
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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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50A LEU* 5.3 0.4 - - - -
79A LEU 2.9 16.0 + - - +
80A ARG 3.9 4.3 - - - +
81A GLU 3.3 0.2 - - - -
82A CYS* 1.3 77.3 - - - +
84A SER* 1.3 58.3 + - - +
86A VAL* 3.4 9.6 + - - +
87A ALA* 2.8 30.1 + - - +
93A ILE* 4.2 13.4 - - + +
121A ASP 4.2 9.4 - - - +
122A LEU* 3.8 26.0 - - + -
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Residues in contact with SER 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 ARG 3.1 14.3 + - - -
81A GLU* 3.4 22.2 + - - -
83A ALA* 1.3 77.0 - - - +
85A ARG* 1.3 56.9 + - - +
87A ALA* 3.4 6.2 + - - +
88A GLN* 2.9 30.8 + - - +
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Residues in contact with ARG 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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51A PHE* 4.6 11.0 - - + -
56A LEU* 3.9 9.9 - - + +
62A HIS* 2.9 57.6 + - + +
63A PHE* 3.9 8.3 - - - -
81A GLU* 2.8 52.9 + - - +
82A CYS 3.7 7.0 - - - +
84A SER* 1.3 71.5 - - - +
86A VAL* 1.3 60.2 + - - +
88A GLN* 3.1 7.9 + - + +
89A ALA* 2.8 30.1 + - - +
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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
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50A LEU* 3.9 33.7 - - + +
51A PHE* 4.4 1.8 - - + +
54A ALA* 4.2 11.2 - - + -
56A LEU* 4.2 11.0 - - + +
82A CYS* 2.9 23.1 + - - +
83A ALA* 3.5 11.4 - - - +
85A ARG* 1.3 76.8 - - - +
87A ALA* 1.3 60.6 + - - +
89A ALA* 3.4 2.0 + - - -
90A GLY 3.3 5.4 + - - -
91A PHE* 3.0 50.5 + - + +
93A ILE* 4.4 18.4 - - + -
156A VAL* 4.8 6.7 - - + -
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Residues in contact with ALA 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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83A ALA 2.8 17.5 + - - +
84A SER* 3.7 7.2 - - - +
86A VAL* 1.3 76.7 - - - +
88A GLN* 1.3 57.9 + - - +
90A GLY* 3.0 19.6 + - - -
91A PHE 3.4 14.8 + - - +
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Residues in contact with GLN 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 SER* 2.9 19.9 + - - +
85A ARG* 3.1 10.3 + - + +
87A ALA* 1.3 77.6 - - - +
89A ALA* 1.3 59.1 + - - +
90A GLY* 3.1 1.3 + - - -
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Residues in contact with ALA 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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54A ALA 5.2 0.4 - - - +
56A LEU* 4.0 23.8 - - + -
85A ARG 2.8 15.8 + - - +
86A VAL 3.7 6.3 - - - +
87A ALA 3.3 0.2 - - - -
88A GLN* 1.3 75.3 - - - +
90A GLY* 1.3 55.9 + - - +
91A PHE* 3.7 21.3 - - + -
158A ARG* 3.2 28.0 + - - -
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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