Contacts of the helix formed by residues 54 - 67 (chain A) in PDB entry 3IAB
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 ASN 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ASN 3.6 3.2 + - - -
53A ASP* 1.3 71.1 - - - +
55A ILE* 1.3 60.9 + - - +
56A LYS* 3.4 7.9 + - - +
57A LYS* 2.9 47.2 + - + +
58A SER* 2.7 32.5 + - - -
94A ILE* 4.9 0.2 - - - -
99R G 3.0 28.2 + - - -
100R A 3.7 18.5 + - - -
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Residues in contact with ILE 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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53A ASP 3.6 0.2 + - - -
54A ASN* 1.3 71.5 - - - +
56A LYS* 1.3 67.8 + - - +
58A SER* 3.2 1.7 + - - -
59A VAL* 2.9 33.4 + - + +
90A LYS* 3.5 27.8 - - - +
93A SER* 4.3 7.9 - - - -
94A ILE* 4.0 21.3 - - + -
97A ILE* 3.7 24.5 - - + -
96R A 3.8 39.3 - - - +
98R G 3.6 19.7 - - - +
99R G 3.6 15.1 + - + +
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Residues in contact with LYS 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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54A ASN* 3.4 9.3 + - - +
55A ILE* 1.3 77.8 - - - +
57A LYS* 1.3 65.5 + - + +
60A ASN* 3.1 21.1 + - - +
98R G 2.8 60.7 + - - +
99R G 3.6 14.5 + - - +
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN* 2.9 33.0 + - + +
55A ILE 3.4 0.2 - - - -
56A LYS* 1.3 76.1 - - + +
58A SER* 1.3 57.8 + - - +
60A ASN* 3.4 12.6 - - - +
61A LYS* 3.1 25.5 + - - +
59R G 5.7 9.3 + - - +
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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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47A HIS* 3.9 18.4 + - - -
53A ASP* 3.9 12.0 + - - +
54A ASN 2.7 23.7 + - - -
55A ILE 3.8 1.6 - - - -
57A LYS* 1.3 77.0 - - - +
59A VAL* 1.3 63.4 + - - +
61A LYS* 3.4 4.2 + - - +
62A LEU* 3.1 27.7 + - - +
94A ILE* 3.7 32.5 - - - +
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Residues in contact with VAL 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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55A ILE* 2.9 29.7 + - + +
58A SER* 1.3 72.3 - - - +
60A ASN* 1.3 65.1 + - - +
62A LEU* 3.2 7.5 + - - +
63A ASP* 3.0 31.1 + - - +
94A ILE* 3.7 26.5 - - + +
97A ILE* 4.0 17.7 - - + -
98A PHE* 3.9 22.2 - - + +
101A GLY* 6.4 0.9 - - - -
98R G 3.6 32.1 - - + +
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Residues in contact with ASN 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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56A LYS* 3.1 29.2 + - - +
57A LYS* 3.4 16.3 - - - +
59A VAL* 1.3 75.6 - - - +
61A LYS* 1.3 62.0 + - - +
63A ASP* 3.3 11.3 + - - +
64A LYS* 3.2 30.6 + - - +
98R G 2.8 19.2 + - - +
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Residues in contact with LYS 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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47A HIS* 4.1 23.1 - - + +
57A LYS 3.1 12.4 + - - +
58A SER* 3.6 9.0 - - - +
59A VAL 3.3 0.4 - - - -
60A ASN* 1.3 78.1 - - - +
62A LEU* 1.3 57.6 + - - +
64A LYS* 3.1 22.8 + - + +
65A GLN* 2.8 49.7 + - - +
68A MSE 5.6 7.5 - - - +
59R G 2.9 47.9 + - - +
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Residues in contact with LEU 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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47A HIS* 3.6 22.2 - - + +
58A SER 3.1 16.0 + - - +
59A VAL* 3.6 3.1 - - - +
61A LYS* 1.3 75.4 - - - +
63A ASP* 1.3 58.0 + - - +
65A GLN* 3.4 20.9 - - - +
66A ILE* 2.9 33.3 + - - +
79A VAL* 3.8 17.9 - - + +
81A ILE* 3.8 26.5 - - + -
94A ILE* 3.8 27.1 - - + +
95A LEU* 4.9 0.2 - - - -
98A PHE* 3.5 37.0 - - + -
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Residues in contact with ASP 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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59A VAL* 3.0 29.2 + - - +
60A ASN* 3.4 14.2 - - - +
61A LYS 3.2 0.2 - - - -
62A LEU* 1.3 77.2 - - - +
64A LYS* 1.3 61.1 + - + +
66A ILE* 3.3 17.0 - - - +
67A ASN* 3.4 16.6 + - - +
98A PHE* 3.2 20.0 - - - +
101A GLY 5.3 5.0 - - - +
102A TYR* 4.7 8.0 - - - -
98R G 4.9 4.0 + - - +
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Residues in contact with LYS 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 ASN* 3.2 21.0 + - - +
61A LYS* 3.1 26.0 + - + +
63A ASP* 1.3 76.9 - - + +
65A GLN* 1.3 61.9 + - - +
67A ASN* 3.2 15.3 + - - +
68A MSE 3.3 33.0 + - + +
59R G 3.7 19.8 + - - -
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Residues in contact with GLN 65 (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 GLN* 3.8 36.3 + - + +
46A TYR 3.1 26.7 + - - -
47A HIS* 3.2 30.4 - - - +
61A LYS* 2.8 38.7 + - + +
62A LEU* 3.4 16.4 + - - +
64A LYS* 1.3 75.1 - - - +
66A ILE* 1.3 61.2 + - - +
67A ASN 3.5 0.5 + - - -
68A MSE 3.5 28.0 + - + +
69A ALA 5.0 0.5 + - - -
77A GLN* 4.9 4.0 - - - +
78A VAL 5.8 0.3 + - - -
79A VAL* 3.8 16.0 - - + +
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Residues in contact with ILE 66 (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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62A LEU 2.9 17.1 + - - +
63A ASP* 3.3 21.1 - - - +
65A GLN* 1.3 76.9 - - - +
67A ASN* 1.3 69.5 + - - +
68A MSE 3.5 0.4 - - - -
77A GLN* 3.0 42.4 - - + +
79A VAL* 3.9 19.9 - - + +
98A PHE* 3.9 16.8 - - + -
102A TYR* 4.0 29.6 - - + +
109A ILE* 4.6 5.2 - - + -
142A VAL* 3.9 22.2 - - + +
143A SER* 4.1 9.0 - - - +
144A ASP* 4.5 6.2 - - - +
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Residues in contact with ASN 67 (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 ASP* 3.4 20.3 + - - +
64A LYS* 3.2 8.7 + - - +
66A ILE* 1.3 91.9 - - - +
68A MSE 1.3 57.4 + - - +
69A ALA 4.7 1.0 - - - +
71A ARG* 5.2 6.4 + - - -
77A GLN* 3.5 16.6 + - - +
102A TYR* 4.8 9.6 + - - -
144A ASP* 5.0 2.3 - - - +
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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