Contacts of the helix formed by residues 54 - 66 (chain A) in PDB entry 4CAA
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 PRO 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN 5.2 1.8 - - - +
33A PHE* 4.8 3.9 - - + -
34A ALA* 3.6 33.9 - - + -
37A LEU* 6.1 0.2 - - + -
52A PHE* 3.5 34.3 - - + +
53A SER* 1.3 81.7 - - - +
55A LEU* 1.3 55.1 + - - +
57A ILE* 2.6 30.9 + - + +
58A SER* 3.0 17.8 + - - +
382B ILE* 3.5 30.1 - - + +
383B PHE 3.5 6.7 - - - +
385B MET* 4.0 5.8 - - + +
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Residues in contact with LEU 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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30A ASN* 4.8 4.5 - - - +
53A SER* 3.5 3.1 - - - +
54A PRO* 1.3 78.2 - - - +
56A SER* 1.3 60.2 + - - +
58A SER* 4.5 5.8 - - - -
59A THR* 2.9 43.7 + - - +
96A PHE* 4.5 7.9 - - + -
99A LEU* 3.9 38.1 - - + -
103A LEU* 4.6 4.9 - - + -
114A MET* 3.6 22.4 - - + +
188A ILE* 4.7 2.7 - - + -
381B ASN* 4.4 13.5 - - + +
382B ILE 3.4 16.7 + - - +
383B PHE* 3.8 31.6 - - + -
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Residues in contact with SER 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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53A SER* 3.0 26.6 + - - -
54A PRO 3.1 0.8 - - - -
55A LEU* 1.3 77.7 - - - +
57A ILE* 1.3 62.6 + - - +
60A ALA* 3.4 18.9 + - - +
114A MET* 4.1 4.4 - - - +
186A ASN* 2.4 36.2 + - - +
188A ILE* 3.8 14.5 - - - +
334A HIS* 4.3 2.7 - - - -
349A ALA* 4.3 0.4 + - - -
350A ALA* 4.1 7.6 - - - -
351A THR* 3.4 21.5 + - - -
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Residues in contact with ILE 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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33A PHE* 4.3 14.1 - - + -
37A LEU* 3.6 25.4 - - + -
52A PHE* 4.0 8.3 - - + -
53A SER 3.4 17.5 - - - +
54A PRO* 2.6 14.0 + - + +
56A SER* 1.3 71.3 - - - +
58A SER* 1.3 63.0 + - - +
60A ALA* 3.3 3.9 + - - +
61A LEU* 3.0 42.5 + - + +
299A LEU* 4.0 24.9 - - + -
303A LEU* 5.4 0.9 - - + -
332A VAL* 5.4 1.3 - - + -
334A HIS* 3.9 23.3 - - + +
351A THR* 3.8 21.3 - - + +
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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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30A ASN* 4.6 16.6 + - - +
33A PHE* 3.5 23.8 - - - +
54A PRO* 3.0 15.6 + - - +
55A LEU* 4.1 6.7 - - - -
57A ILE* 1.3 77.4 - - - +
59A THR* 1.3 56.9 + - - +
62A ALA* 2.8 33.3 + - - +
80A LEU* 3.9 19.5 - - - +
82A PHE* 6.2 0.2 - - - -
96A PHE* 4.0 18.2 - - - -
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Residues in contact with THR 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 LEU* 2.9 27.1 + - - +
56A SER 4.4 0.2 - - - -
58A SER* 1.3 75.4 - - - +
60A ALA* 1.3 58.5 + - - +
62A ALA* 3.7 1.7 - - - +
63A PHE* 2.9 29.8 + - - +
96A PHE* 3.4 27.7 - - + -
99A LEU* 4.9 0.7 - - - +
100A LEU* 4.2 11.2 - - + -
114A MET* 4.0 4.6 - - - -
116A ASN* 3.6 30.7 - - - +
138A TYR* 4.0 11.8 - - + -
186A ASN* 4.1 12.1 - - - +
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Residues in contact with ALA 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 SER 3.4 16.5 + - - +
57A ILE 3.3 5.3 + - - +
59A THR* 1.3 75.5 - - - +
61A LEU* 1.3 65.8 + - + +
63A PHE* 3.1 23.2 - - - +
64A LEU* 3.1 7.8 + - - +
184A LEU* 4.8 5.7 - - + +
185A VAL 5.4 1.3 - - - -
186A ASN* 4.0 18.3 - - + +
351A THR* 4.2 21.5 - - + +
353A VAL* 4.7 13.6 - - + +
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Residues in contact with LEU 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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33A PHE* 4.4 0.7 - - + -
57A ILE* 3.0 30.2 + - + +
58A SER 4.2 1.3 - - - +
60A ALA* 1.3 73.3 - - + +
62A ALA* 1.3 62.4 + - - +
64A LEU* 2.8 45.9 + - + +
65A SER* 3.1 7.1 + - - -
76A ILE* 4.1 10.2 - - + +
80A LEU* 4.0 28.0 - - + -
303A LEU* 3.8 43.5 - - + -
308A ILE* 4.2 12.6 - - + -
332A VAL* 4.5 15.3 - - + -
353A VAL* 4.5 6.1 - - + -
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Residues in contact with ALA 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 2.8 20.4 + - - +
59A THR* 3.7 4.3 - - - +
61A LEU* 1.3 75.7 - - - +
63A PHE* 1.3 64.2 + - - +
65A SER* 2.9 28.6 + - - -
77A LEU* 5.8 0.9 - - + -
80A LEU* 4.0 11.8 - - + +
92A ILE* 5.2 4.7 - - + -
93A HIS* 3.6 8.7 - - - +
96A PHE* 3.6 23.6 - - + -
138A TYR* 3.6 17.3 - - - +
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Residues in contact with PHE 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 THR 2.9 16.1 + - - +
60A ALA* 3.1 15.0 - - - +
62A ALA* 1.3 73.9 - - - +
64A LEU* 1.3 63.6 + - - +
65A SER 3.0 1.2 + - - -
66A LEU* 3.1 21.4 + - + +
116A ASN* 4.1 23.6 - - + -
117A ALA 3.9 11.4 - - - -
118A MET* 4.3 5.4 - - + -
130A PHE* 4.3 11.6 - + - -
134A ALA* 3.9 20.9 - - + -
138A TYR* 4.0 26.6 - + + -
140A SER* 3.2 30.3 - - - -
184A LEU* 3.6 40.4 - - + -
185A VAL 5.0 3.4 - - - -
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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 ALA 3.1 6.1 + - - +
61A LEU* 2.8 35.3 + - + +
63A PHE* 1.3 80.4 - - - +
65A SER* 1.3 60.5 + - - +
66A LEU 3.1 1.0 + - - -
67A GLY* 3.1 12.1 + - - -
68A ALA* 3.5 6.7 + - - +
76A ILE* 3.9 24.7 - - + -
130A PHE* 5.4 0.9 - - - -
184A LEU* 3.9 25.3 - - + +
308A ILE* 6.1 1.3 - - + -
311A ALA* 5.3 1.3 - - + -
318A LEU* 4.5 17.3 - - + -
321A ILE* 5.5 4.0 - - + +
329A VAL* 4.0 20.9 - - + -
332A VAL* 5.9 0.4 - - + -
353A VAL* 4.3 11.2 - - + -
355A ILE* 4.2 17.3 - - + -
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Residues in contact with SER 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 LEU 3.1 3.9 + - - -
62A ALA* 2.9 19.6 + - - -
64A LEU* 1.3 76.3 - - - +
66A LEU* 1.3 61.5 + - - -
67A GLY 2.9 1.9 + - - -
68A ALA* 2.9 28.9 + - - +
73A LEU* 4.2 10.6 + - - +
76A ILE* 3.3 26.5 - - - +
77A LEU* 3.5 21.8 - - - +
89A GLU* 4.7 1.8 - - - +
93A HIS* 3.6 16.8 - - - -
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Residues in contact with LEU 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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63A PHE* 3.1 18.5 + - + +
65A SER* 1.3 76.1 - - - +
67A GLY* 1.3 58.2 + - - +
68A ALA 4.6 1.5 - - - +
69A HIS* 5.3 1.4 - - - -
89A GLU* 5.4 2.2 - - - -
93A HIS* 3.0 48.2 - - + +
130A PHE* 3.6 25.5 - - + +
133A ASP* 3.8 36.1 - - + +
134A ALA* 3.9 19.7 - - + +
137A LEU* 4.6 3.1 - - + -
138A TYR* 4.1 15.0 - - + -
320A GLY* 4.1 9.0 - - - -
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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