Contacts of the helix formed by residues 72 - 86 (chain A) in PDB entry 1IV4
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 ARG 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY 4.6 13.9 + - - -
36A ASP* 3.9 10.8 - - + +
70A GLY 3.8 1.0 + - - -
71A GLU* 1.3 79.0 + - - +
73A SER* 1.3 66.6 + - - +
74A GLU* 4.2 22.7 + - + +
75A VAL* 3.0 29.2 + - + +
76A PHE* 4.0 2.6 + - - -
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Residues in contact with SER 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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35A SER* 4.9 0.7 - - - -
36A ASP* 2.4 39.9 + - - -
38A ASP* 4.1 1.6 - - - -
41A MET* 3.6 30.1 - - - +
42A HIS* 3.0 22.6 + - - -
45A THR* 4.6 0.7 + - - -
71A GLU 3.7 0.6 + - - -
72A ARG* 1.3 73.1 - - - +
74A GLU* 1.3 61.8 + - - +
76A PHE* 3.1 26.8 + - - +
77A LEU* 3.2 11.6 + - - +
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Residues in contact with GLU 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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22A GLY* 5.5 8.2 - - - +
41A MET* 4.0 15.4 - - + +
72A ARG* 3.2 22.0 + - + +
73A SER* 1.3 76.0 - - - +
75A VAL* 1.3 59.0 + - + +
77A LEU* 3.7 2.8 - - + +
78A ARG* 2.5 75.2 + - + +
118A ARG* 4.6 6.5 + - - -
119A LEU* 3.5 33.3 - - + +
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Residues in contact with VAL 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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68A TRP* 3.7 29.6 - - + -
71A GLU* 3.7 31.0 - - + +
72A ARG* 3.0 23.5 + - + +
74A GLU* 1.3 81.4 - - + +
76A PHE* 1.3 56.5 + - + +
78A ARG* 3.4 6.7 + - - +
79A GLU* 3.0 26.3 + - - +
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Residues in contact with PHE 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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35A SER* 5.6 6.5 - - - -
42A HIS* 4.6 13.9 - + + -
45A THR* 4.0 8.5 - - + +
57A ILE* 5.3 4.5 - - + -
61A PHE* 3.6 56.3 - + + -
68A TRP* 3.6 44.9 - + + -
70A GLY 5.8 0.2 - - - -
71A GLU* 3.9 27.4 - - + -
72A ARG 4.4 0.2 - - - -
73A SER* 3.1 30.7 + - - +
75A VAL* 1.3 76.3 - - - +
77A LEU* 1.3 66.1 + - - +
79A GLU 3.2 0.7 + - - -
80A ALA* 2.8 24.9 + - - +
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Residues in contact with LEU 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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41A MET* 3.9 26.2 - - + +
44A LEU* 3.9 24.0 - - + -
45A THR* 3.3 25.2 + - - +
48A LEU* 3.8 23.1 - - + -
73A SER 3.2 9.2 + - - +
74A GLU* 3.3 7.8 + - + +
76A PHE* 1.3 79.9 - - - +
78A ARG* 1.3 61.7 + - + +
80A ALA* 3.1 2.8 + - - +
81A MET* 2.7 41.9 + - - +
119A LEU* 4.1 26.7 - - + +
120A MET* 4.6 11.2 - - + -
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Residues in contact with ARG 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 GLU* 2.5 59.0 + - + +
75A VAL* 3.8 7.2 - - - +
77A LEU* 1.3 75.6 - - + +
79A GLU* 1.3 58.3 + - - +
81A MET* 3.3 16.7 + - + +
82A ARG* 2.9 26.5 + - - +
118A ARG* 4.2 15.4 + - - +
119A LEU* 3.8 33.6 + - - +
121A ARG* 6.0 2.0 - - - +
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Residues in contact with GLU 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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61A PHE* 3.6 26.2 - - + -
68A TRP* 3.8 22.4 - - + -
75A VAL 3.0 17.5 + - - +
76A PHE 3.2 4.0 + - - +
78A ARG* 1.3 74.9 - - - +
80A ALA* 1.3 66.2 + - - +
82A ARG* 2.8 49.7 + - - +
83A LEU* 2.9 40.1 + - + +
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Residues in contact with ALA 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 THR* 3.7 20.2 - - + -
48A LEU* 4.2 16.2 - - + -
49A LEU* 3.8 25.4 - - + -
61A PHE* 4.3 1.7 - - + -
76A PHE 2.8 13.6 + - - +
77A LEU 3.5 7.4 - - - +
79A GLU* 1.3 76.7 - - - +
81A MET* 1.3 63.8 + - - +
83A LEU* 3.2 4.2 + - - +
84A VAL* 3.0 29.3 + - - +
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Residues in contact with MET 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* 4.1 14.4 - - + -
77A LEU* 2.7 39.6 + - - +
78A ARG* 3.5 13.2 - - + +
80A ALA* 1.3 77.0 - - - +
82A ARG* 1.3 66.2 + - - +
83A LEU 3.3 0.2 + - - -
84A VAL* 3.5 8.0 - - - +
85A GLU* 2.9 50.1 + - - +
91A LEU* 5.2 6.7 - - + -
119A LEU 3.7 25.1 - - - +
120A MET* 3.9 27.1 - - - +
121A ARG* 4.7 10.5 - - - +
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Residues in contact with ARG 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 ARG 2.9 14.4 + - - +
79A GLU* 2.8 46.4 + - - +
81A MET* 1.3 77.2 - - - +
83A LEU* 1.3 72.8 + - - +
85A GLU* 3.8 9.6 - - - +
86A ALA* 3.0 35.7 + - + +
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Residues in contact with LEU 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* 4.3 7.9 - - + -
54A LEU* 3.9 15.7 - - + -
60A LEU* 3.7 31.0 - - + -
61A PHE* 5.1 0.4 - - + -
79A GLU* 2.9 36.3 + - + +
80A ALA* 3.6 4.3 - - - +
82A ARG* 1.3 99.0 - - - +
84A VAL* 1.3 63.5 + - - +
86A ALA* 3.5 2.4 + - + -
87A ARG* 2.9 48.5 + - - +
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Residues in contact with VAL 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* 3.5 35.0 - - + +
49A LEU* 4.9 0.4 - - - -
52A TYR* 3.6 23.7 - - + -
54A LEU* 4.1 14.4 - - + -
80A ALA 3.0 15.5 + - - +
81A MET* 3.5 14.1 - - - +
83A LEU* 1.3 77.7 - - - +
85A GLU* 1.3 64.0 + - + +
87A ARG* 2.9 24.0 + - - +
88A GLY 3.3 0.5 + - - -
89A ALA* 3.1 28.0 + - + +
91A LEU* 6.2 0.9 - - + -
150A LEU* 4.3 12.1 - - + -
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Residues in contact with GLU 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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81A MET* 2.9 42.8 + - - +
82A ARG* 3.8 7.6 - - - +
84A VAL* 1.3 80.8 - - + +
86A ALA* 1.3 56.9 + - - +
87A ARG 3.0 0.2 - - - -
88A GLY* 3.0 19.6 + - - -
89A ALA* 3.8 20.8 - - + +
90A LYS* 5.7 1.1 - - - -
91A LEU* 5.8 5.8 + - - +
121A ARG* 2.9 29.3 + - - -
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Residues in contact with ALA 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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82A ARG* 3.0 26.8 + - + +
83A LEU* 3.8 7.0 - - + +
84A VAL 3.2 0.4 - - - -
85A GLU* 1.3 76.6 - - - +
87A ARG* 1.3 68.5 + - - +
88A GLY 3.3 1.7 + - - -
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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