Contacts of the helix formed by residues 50 - 67 (chain A) in PDB entry 3N4U
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 HIS 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.4 42.1 - - + +
32A ASN* 2.5 24.2 + - + +
33A ASP* 3.3 27.6 - - - -
48A PRO* 3.4 2.4 - - - +
49A LYS* 1.3 82.7 - - + +
51A SER* 1.3 61.9 + - - +
52A ARG* 3.2 14.8 - - + +
53A GLY* 2.9 28.2 + - - -
54A SER* 2.8 27.2 + - - -
88A TYR* 3.2 12.8 + - - -
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Residues in contact with SER 51 (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 HIS* 1.3 74.8 - - - +
52A ARG* 1.3 63.0 + - - +
54A SER* 3.1 5.4 + - - -
55A THR* 2.9 31.5 + - - -
87A THR* 3.1 45.3 - - - +
88A TYR* 3.8 10.0 - - - -
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP* 5.4 0.9 - - - +
50A HIS* 3.2 14.2 + - + +
51A SER* 1.3 84.6 + - - +
53A GLY* 1.3 58.6 + - - +
55A THR* 3.2 39.9 + - - +
56A ASN* 2.9 48.0 + - - +
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Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP* 3.7 30.3 - - - -
34A CYS* 4.2 5.7 - - - -
48A PRO* 3.9 5.8 - - - -
50A HIS* 2.9 25.4 + - - -
52A ARG* 1.3 76.4 - - - +
54A SER* 1.3 55.9 + - - +
56A ASN* 3.4 3.3 + - - +
57A LEU* 3.0 27.7 + - - +
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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
----------------------------------------------------------
48A PRO* 3.6 12.0 - - - +
50A HIS 2.8 15.2 + - - -
51A SER 3.1 8.3 + - - -
53A GLY* 1.3 68.8 - - - +
55A THR* 1.3 61.4 + - - +
57A LEU* 3.4 3.1 + - - +
58A PHE* 3.0 27.9 + - - +
88A TYR* 3.4 29.0 - - - +
89A GLN 3.2 6.2 + - - -
90A MET* 2.8 41.3 + - - +
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Residues in contact with THR 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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51A SER 2.9 15.8 + - - -
52A ARG* 3.3 41.0 + - - +
54A SER* 1.3 73.9 - - - +
56A ASN* 1.3 63.8 + - - +
58A PHE* 3.2 6.0 + - - +
59A ASN* 2.8 42.2 + - - +
87A THR 5.3 1.7 + - - -
89A GLN* 3.0 32.4 + - - +
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Residues in contact with ASN 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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33A ASP* 2.9 30.7 + - + +
52A ARG* 2.9 32.8 + - - +
53A GLY 3.6 5.8 - - - +
55A THR* 1.3 80.8 - - - +
57A LEU* 1.3 56.0 + - - +
59A ASN* 3.2 15.4 - - - +
60A GLU* 2.8 27.9 + - - +
219A GLY* 3.1 28.1 + - - +
220A ASP* 4.1 8.8 + - - -
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Residues in contact with LEU 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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34A CYS* 4.6 8.1 - - - -
46A LYS* 3.5 40.2 - - + +
48A PRO* 4.3 7.9 - - + -
53A GLY 3.0 16.6 + - - +
54A SER* 3.8 5.2 - - - +
55A THR 3.2 0.2 - - - -
56A ASN* 1.3 75.2 - - - +
58A PHE* 1.3 66.4 + - - +
60A GLU* 3.3 12.9 + - - +
61A VAL* 2.9 25.2 + - - +
90A MET* 3.9 16.2 - - + +
92A PHE* 3.8 10.3 - - - -
93A ALA* 3.7 16.8 - - + +
95A PHE* 3.8 28.5 - - + -
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Residues in contact with PHE 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 3.0 14.7 + - - +
55A THR 3.3 7.0 - - - +
57A LEU* 1.3 75.9 - - - +
59A ASN* 1.3 78.8 + - - +
61A VAL* 3.4 3.5 + - - +
62A ASN* 3.1 50.5 + - - -
89A GLN* 3.7 48.5 - - + -
90A MET* 4.0 29.5 - - + +
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Residues in contact with ASN 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 THR* 2.8 28.9 + - - +
56A ASN* 3.2 21.7 - - - +
58A PHE* 1.3 90.4 - - - +
60A GLU* 1.3 65.4 + - - +
62A ASN* 3.2 5.7 + - - +
63A ILE* 2.8 34.7 + - + +
141A ASN* 5.5 4.2 + - - -
142A LEU* 4.2 26.8 - - + +
218A PHE 5.5 0.7 - - - +
219A GLY 5.0 3.6 - - - +
221A ALA 5.2 4.7 - - - +
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Residues in contact with GLU 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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46A LYS* 3.1 36.2 + - - +
56A ASN 2.8 18.1 + - - +
57A LEU* 3.3 12.0 + - + +
59A ASN* 1.3 71.3 - - - +
61A VAL* 1.3 65.5 + - - +
63A ILE* 3.2 2.8 + - - +
64A LEU* 2.8 47.7 + - + +
76A PRO* 5.5 2.1 - - - +
95A PHE* 3.8 15.3 - - + -
217A ASP* 3.4 4.9 + - - -
218A PHE* 2.7 44.5 + - + +
219A GLY* 3.6 12.6 + - - +
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Residues in contact with VAL 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 LEU 2.9 16.9 + - - +
58A PHE 3.6 8.1 - - - +
60A GLU* 1.3 77.4 - - - +
62A ASN* 1.3 67.8 + - - +
64A LEU* 3.8 1.0 - - - +
65A LYS* 3.0 42.9 + - - +
78A VAL* 3.9 25.2 - - + +
81A THR* 4.2 12.3 - - + -
90A MET* 4.3 18.2 - - + -
93A ALA* 3.6 29.8 - - + -
95A PHE* 4.5 8.7 - - + -
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Residues in contact with ASN 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 PHE* 3.1 57.9 + - - +
59A ASN* 3.7 5.3 - - - +
61A VAL* 1.3 80.7 - - - +
63A ILE* 1.3 64.5 + - + +
65A LYS* 3.5 25.2 + - - +
66A ARG* 3.0 31.2 + - - +
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Residues in contact with ILE 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 ASN* 2.8 24.5 + - + +
60A GLU* 3.8 4.0 - - - +
62A ASN* 1.3 78.8 - - + +
64A LEU* 1.3 63.1 + - - +
66A ARG* 3.1 7.8 + - - +
67A ILE* 3.0 49.6 + - + +
138A PHE* 4.6 17.3 - - + -
142A LEU* 4.5 16.6 - - + -
193A LEU* 4.5 19.1 - - + -
218A PHE* 4.5 16.6 - - + +
221A ALA* 3.5 39.5 - - + +
222A ALA* 4.9 0.2 - - - -
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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 GLU* 2.8 33.3 + - + +
63A ILE* 1.3 74.9 - - - +
65A LYS* 1.3 65.4 + - - +
67A ILE* 3.9 3.1 - - + +
68A HIS* 3.1 26.7 + - - +
75A ILE* 3.9 21.2 - - + +
76A PRO* 3.7 32.6 - - + +
78A VAL* 3.8 13.9 - - + -
95A PHE* 3.6 37.7 - - + -
218A PHE* 3.8 31.9 - - + -
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Residues in contact with LYS 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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61A VAL* 3.0 30.4 + - + +
62A ASN* 3.8 28.4 + - - +
64A LEU* 1.3 77.5 - - - +
66A ARG* 1.3 62.2 + - - +
67A ILE 3.5 0.2 + - - -
68A HIS* 3.6 15.1 - - - +
78A VAL* 4.1 21.1 - - + +
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Residues in contact with ARG 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 ASN* 3.0 25.0 + - - +
63A ILE* 3.1 6.7 + - - +
65A LYS* 1.3 79.5 - - - +
67A ILE* 1.3 64.1 + - + +
68A HIS 3.4 0.8 + - - +
70A LYS* 4.4 9.9 - - - +
133A ILE* 6.1 2.9 - - + -
137A GLY 3.1 26.8 + - - -
138A PHE* 3.5 45.3 - - + +
142A LEU* 5.6 0.4 - - - +
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Residues in contact with ILE 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 ILE* 3.0 33.8 + - + +
64A LEU* 4.0 2.7 - - - +
66A ARG* 1.3 87.3 - - + +
68A HIS* 1.3 65.9 + - - +
69A ASN 3.3 0.9 + - - -
70A LYS* 3.0 23.6 + - + +
71A LEU* 4.1 13.1 + - + +
75A ILE* 3.7 22.6 - - + +
130A LEU* 4.7 7.2 - - + -
133A ILE* 3.5 33.7 - - + -
138A PHE* 5.8 0.4 - - + -
193A LEU* 4.1 12.6 - - + -
218A PHE* 4.0 23.8 - - + -
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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