Contacts of the helix formed by residues 53 - 64 (chain A) in PDB entry 1INZ
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU 3.8 2.4 + - - -
47A THR* 3.3 23.1 - - + +
49A ASN 4.2 2.0 - - - +
50A VAL 4.0 9.4 - - - +
51A VAL 2.7 4.6 + - - +
52A ALA* 1.3 75.8 - - - +
54A SER* 1.3 80.2 + - - +
56A ILE* 2.9 22.7 + - - +
57A MET* 3.2 27.5 + - + +
91A ARG* 3.3 51.6 - - + +
92A VAL* 3.4 39.5 - - + -
95A GLN* 4.3 21.3 - - + -
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Residues in contact with SER 54 (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 VAL 3.9 10.0 + - - -
51A VAL* 2.7 14.4 + - - -
53A PHE* 1.3 89.8 - - - +
55A GLU* 1.3 57.6 + - - -
57A MET* 5.3 2.7 - - - -
58A SER* 2.5 38.2 + - - -
95A GLN* 5.6 3.1 - - - -
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Residues in contact with GLU 55 (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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18A SER* 4.0 8.8 + - - -
20A ALA* 4.8 0.2 - - + -
21A GLU* 4.4 32.5 - - + +
51A VAL* 3.2 35.4 - - + +
52A ALA* 3.0 10.0 + - - +
54A SER* 1.3 78.2 - - - +
56A ILE* 1.3 63.6 + - - +
58A SER* 4.0 5.1 - - - -
59A MET* 3.5 27.6 + - - +
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Residues in contact with ILE 56 (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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20A ALA* 3.4 15.7 - - + -
24A VAL* 3.3 18.5 - - + +
43A ILE* 3.1 49.8 - - + +
46A LEU* 3.3 14.8 - - + -
47A THR* 3.6 8.3 - - + +
52A ALA 2.8 33.0 + - - +
53A PHE* 2.9 12.4 + - - +
55A GLU* 1.3 76.8 - - - +
57A MET* 1.3 71.2 + - + +
58A SER 3.0 1.8 + - - -
59A MET 3.2 3.1 + - - -
60A ILE* 3.0 23.4 + - + +
84A LEU* 3.3 17.3 - - + -
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Residues in contact with MET 57 (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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53A PHE* 3.2 32.1 + - + +
54A SER* 4.8 1.3 - - - +
56A ILE* 1.3 82.6 - - + +
58A SER* 1.3 59.0 + - - +
60A ILE* 3.0 14.0 + - - +
61A TRP* 2.6 69.9 + - + +
81A MET* 4.1 26.7 - - + -
84A LEU* 5.1 2.0 - - - -
85A ILE* 4.9 0.7 - - + -
92A VAL* 3.9 35.7 - - + +
95A GLN* 3.9 21.1 - - + +
96A CYS* 4.6 3.6 - - - +
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Residues in contact with SER 58 (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 SER* 2.5 27.4 + - - -
55A GLU* 4.0 5.8 - - - -
56A ILE 3.0 0.6 + - - -
57A MET* 1.3 78.2 - - - +
59A MET* 1.3 64.7 + - - -
61A TRP* 2.9 23.6 + - - +
62A LYS* 3.3 20.6 + - - +
95A GLN* 5.5 0.7 + - - -
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Residues in contact with MET 59 (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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21A GLU* 3.2 53.6 - - + +
22A ILE* 6.1 0.9 - - + -
24A VAL* 3.8 14.3 - - + +
25A ARG* 3.9 31.6 - - + +
55A GLU* 3.5 12.7 + - - +
56A ILE 3.2 3.4 + - - +
58A SER* 1.3 79.6 - - - +
60A ILE* 1.3 62.5 + - - +
62A LYS* 3.6 18.3 + - + +
63A ARG* 3.4 33.7 + - + +
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Residues in contact with ILE 60 (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 VAL* 3.5 4.0 - - + -
28A THR* 4.6 4.9 - - + -
56A ILE* 3.0 36.6 + - + +
57A MET* 3.2 17.0 - - - +
58A SER 3.0 0.2 - - - -
59A MET* 1.3 80.7 - - - +
61A TRP* 1.3 60.0 + - + +
63A ARG* 5.1 0.9 - - - -
64A LEU* 2.8 49.3 + - + +
77A ALA* 3.8 10.0 - - - +
80A LEU* 3.0 51.6 - - + -
81A MET* 3.7 23.3 - - + -
84A LEU* 3.8 4.5 - - + -
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Residues in contact with TRP 61 (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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57A MET* 2.6 62.7 + - + +
58A SER* 2.9 11.8 + - - +
60A ILE* 1.3 77.7 - - - +
62A LYS* 1.3 67.9 + - + +
64A LEU* 3.1 29.4 - - + +
65A ASN* 3.3 10.2 + - - +
81A MET* 3.0 26.0 - - - -
95A GLN* 4.2 12.5 + - + +
96A CYS* 4.9 2.7 - - - -
99A ASN* 4.0 33.0 - - + +
102A ALA* 3.4 29.2 - - + -
103A VAL* 3.2 24.7 - - + -
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Residues in contact with LYS 62 (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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58A SER* 3.3 26.8 + - - +
59A MET* 3.8 17.2 - - + +
61A TRP* 1.3 79.6 - - + +
63A ARG* 1.3 62.9 + - + +
64A LEU 2.9 5.4 + - - -
65A ASN* 3.0 21.2 + - - +
66A ASP* 3.8 1.9 + - - +
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Residues in contact with ARG 63 (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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25A ARG* 2.7 63.5 - - - +
28A THR* 4.8 17.0 + - + +
29A SER* 4.9 11.9 + - - -
59A MET* 3.4 23.2 + - + +
60A ILE* 4.0 2.2 - - - +
62A LYS* 1.3 76.7 - - + +
64A LEU* 1.3 59.5 + - - +
66A ASP* 3.5 15.4 - - - +
73A HIS* 3.5 37.4 + - + +
74A VAL* 3.3 24.9 + - - +
77A ALA* 4.2 6.5 - - + -
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Residues in contact with LEU 64 (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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60A ILE* 2.8 28.8 + - + +
61A TRP* 3.1 27.4 - - + +
62A LYS 2.9 0.4 + - - -
63A ARG* 1.3 80.8 - - - +
65A ASN* 1.3 56.0 + - + +
74A VAL* 2.9 27.5 - - + +
77A ALA* 3.2 21.1 - - + +
78A MET* 3.7 8.5 - - + +
81A MET* 3.4 36.8 - - + -
102A ALA 5.6 2.2 - - - +
105A THR* 5.6 0.8 - - - +
106A LEU* 3.1 49.2 - - + +
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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