Contacts of the helix formed by residues 53 - 65 (chain A) in PDB entry 3CWM
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 SER 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 1.3 74.1 - - - +
54A PRO* 1.3 64.5 - - - +
55A VAL* 3.7 3.6 + - - +
56A SER* 3.0 35.5 + - - -
57A ILE* 3.2 26.5 + - - +
188A ILE* 3.8 8.8 - - - +
334A HIS* 3.1 14.3 + - - -
336A ALA* 4.4 0.6 - - - +
383A LEU* 2.6 19.8 + - - +
384A PHE* 3.9 13.2 - - - -
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Residues in contact with PRO 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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30A LEU* 4.4 5.6 - - + +
33A PHE* 3.6 13.6 - - + -
34A ALA* 3.5 40.2 - - + +
52A PHE* 3.4 28.5 - - + +
53A SER* 1.3 81.9 - - - +
55A VAL* 1.3 62.0 + - - +
57A ILE* 5.1 0.2 - - + -
58A ALA* 3.0 27.0 + - - +
382A PRO* 3.3 29.4 - - + +
383A LEU 3.4 4.3 - - - +
384A PHE* 3.7 9.9 - - - -
385A MET* 4.5 1.1 - - + +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.3 10.8 - - + -
53A SER* 4.0 5.2 - - - +
54A PRO* 1.3 76.2 - - - +
56A SER* 1.3 55.3 + - - +
59A THR* 2.8 46.1 + - - +
99A LEU* 3.8 23.3 - - + -
100A LEU* 6.5 0.4 - - + -
103A LEU* 3.9 22.7 - - + -
381A SER* 3.8 21.5 - - - -
382A PRO* 3.1 31.1 + - + +
383A LEU* 4.0 9.4 - - + -
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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 32.8 + - - -
55A VAL* 1.3 78.6 - - - +
57A ILE* 1.3 59.7 + - - +
59A THR* 4.1 4.0 - - - -
60A ALA 3.3 11.8 + - - -
114A THR* 3.7 16.6 + - - -
116A ASN* 4.3 0.9 + - - -
186A ASN* 2.6 47.7 + - - -
187A TYR 4.1 4.7 + - - -
188A ILE* 4.1 8.9 - - - +
334A HIS* 4.0 3.1 - - - -
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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* 3.8 21.3 - - + -
37A LEU* 4.1 18.4 - - + -
52A PHE* 4.4 6.5 - - + -
53A SER 3.2 21.9 + - - +
54A PRO 4.1 1.3 - - - +
56A SER* 1.3 75.5 - - - +
58A ALA* 1.3 66.3 + - - +
60A ALA* 3.2 3.7 + - - +
61A PHE* 3.0 25.0 + - + +
80A LEU* 5.3 0.4 - - + -
186A ASN* 4.3 2.2 - - - +
297A TYR* 5.9 0.4 - - + -
299A LEU* 4.2 21.8 - - + -
303A LEU* 4.1 23.1 - - + -
334A HIS* 3.5 44.0 - - + +
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Residues in contact with ALA 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 LEU* 3.7 23.6 - - + -
33A PHE* 4.0 11.9 - - + -
54A PRO 3.0 19.5 + - - +
55A VAL 3.9 0.4 - - - +
57A ILE* 1.3 74.2 - - - +
59A THR* 1.3 57.1 + - - +
61A PHE* 3.0 2.3 + - - -
62A ALA* 2.7 35.5 + - - +
80A LEU* 3.7 22.5 - - + +
96A PHE* 3.8 12.6 - - + -
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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 VAL* 2.8 33.9 + - - +
56A SER* 4.1 5.6 - - - +
58A ALA* 1.3 77.0 - - - +
60A ALA* 1.3 61.2 + - - +
62A ALA* 3.5 2.6 - - - +
63A MET* 3.1 22.9 + - - +
96A PHE* 3.4 24.5 + - + -
99A LEU* 4.7 2.4 - - - +
100A LEU* 3.8 40.1 - - + +
116A ASN* 5.0 7.2 - - - +
138A TYR* 3.8 9.2 - - + +
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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 3.3 12.8 + - - +
57A ILE* 3.2 6.1 + - - +
58A ALA 3.2 1.0 - - - -
59A THR* 1.3 78.4 - - - +
61A PHE* 1.3 67.6 + - + +
63A MET* 3.3 13.6 + - - +
64A LEU* 3.0 24.6 + - - +
116A ASN* 3.3 37.5 - - - +
184A LEU* 4.3 9.9 - - + +
186A ASN* 3.6 6.1 - - + +
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Residues in contact with PHE 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 ILE* 3.0 20.0 + - + +
58A ALA 3.0 3.7 + - - +
60A ALA* 1.3 79.0 - - + +
62A ALA* 1.3 60.8 + - - +
63A MET 3.2 0.2 - - - -
64A LEU* 3.7 27.8 - - + +
65A SER* 3.0 28.2 + - - -
76A ILE* 3.3 32.8 - - + +
80A LEU* 4.3 10.8 - - + -
184A LEU* 4.1 13.7 - - + -
299A LEU* 3.8 19.1 - - + -
303A LEU* 3.7 29.8 - - + -
308A ILE* 4.9 3.8 - - + -
311A VAL* 4.7 2.9 - - + -
312A PHE* 3.7 31.2 - + - -
329A LEU* 4.1 4.5 - - + -
332A ALA* 4.0 13.5 - - + -
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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 ALA 2.7 20.8 + - - +
59A THR 3.5 6.5 - - - +
61A PHE* 1.3 73.4 - - - +
63A MET* 1.3 61.6 + - - +
65A SER* 2.6 27.5 + - - -
66A LEU* 3.6 0.7 + - - +
77A LEU* 4.5 4.9 - - + -
80A LEU* 3.9 7.5 - - + +
93A HIS* 3.6 11.6 - - + +
96A PHE* 3.6 34.5 - - + -
138A TYR* 3.8 10.8 - - - +
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Residues in contact with MET 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 3.1 12.6 + - - +
60A ALA* 3.3 24.7 - - + +
61A PHE 3.2 0.4 - - - -
62A ALA* 1.3 76.8 - - - +
64A LEU* 1.3 68.7 + - - +
66A LEU* 3.0 23.0 + - + +
116A ASN* 4.4 13.5 - - - +
118A LEU* 4.3 26.9 - - + -
130A PHE* 3.8 5.2 - - - -
134A VAL* 3.9 25.8 - - + -
138A TYR* 3.6 37.9 - - + -
140A SER* 3.4 31.9 - - - -
184A LEU* 4.7 1.6 - - + -
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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 3.0 17.2 + - - +
61A PHE* 3.7 28.9 - - + +
63A MET* 1.3 79.4 - - + +
65A SER* 1.3 56.1 + - - +
67A GLY* 3.0 20.1 + - - -
68A THR* 3.6 9.6 - - + +
76A ILE* 4.8 2.5 - - + -
118A LEU* 5.3 2.0 - - + -
130A PHE* 4.0 13.3 - - + -
182A PHE* 3.8 35.4 - - + -
184A LEU* 4.5 9.9 - - + -
311A VAL* 4.2 16.4 - - + -
318A LEU* 4.2 13.2 - - + -
329A LEU* 3.6 26.2 - - + -
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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 PHE 3.0 15.4 + - - -
62A ALA 2.6 20.3 + - - -
63A MET 3.1 0.4 - - - -
64A LEU* 1.3 74.4 - - - +
66A LEU* 1.3 61.4 + - - +
67A GLY 3.1 0.2 - - - -
68A THR* 2.9 31.5 + - - +
73A HIS* 3.3 20.6 - - - -
76A ILE* 4.3 10.5 - - - -
77A LEU* 3.8 20.0 - - - +
93A HIS* 3.6 15.2 + - - -
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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