Contacts of the helix formed by residues 55 - 67 (chain A) in PDB entry 3EWS
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 ASP 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A MET 4.2 1.2 - - - -
54A GLU* 1.3 70.1 - - - +
56A ARG* 1.3 63.3 + - - +
57A ALA* 3.1 4.3 + - - -
58A ALA* 3.3 23.6 + - - +
59A GLN* 3.6 30.4 + - - +
392A VAL* 3.8 24.2 - - + +
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Residues in contact with ARG 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 MET 5.6 1.4 + - - -
54A GLU* 3.0 28.7 - - + +
55A ASP* 1.3 78.3 - - - +
57A ALA* 1.3 63.2 + - - +
59A GLN* 3.4 16.5 + - - +
60A SER* 3.0 24.3 + - - -
245A ASP* 3.7 42.8 + - - +
246A VAL* 4.2 24.1 - - + +
248A ILE* 4.8 6.9 - - - +
249A ALA* 5.0 1.8 - - + -
276A THR* 4.3 17.8 + - - +
278A GLU* 3.8 20.8 + - - +
281A VAL* 5.5 0.4 - - - +
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Residues in contact with ALA 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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54A GLU 4.9 0.8 + - - -
55A ASP 3.1 1.4 + - - -
56A ARG* 1.3 77.0 - - - +
58A ALA* 1.3 66.8 + - - +
60A SER* 3.0 5.8 + - - -
61A LEU* 2.9 24.0 + - - +
171A THR* 4.0 28.3 - - + +
174A LEU* 4.3 6.9 - - + +
246A VAL* 3.9 18.1 - - + +
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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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55A ASP* 3.3 21.1 + - - +
57A ALA* 1.3 77.0 - - - +
59A GLN* 1.3 59.0 + - + +
61A LEU* 3.3 7.3 + - - +
62A LEU* 2.9 30.1 + - - +
369A VAL* 4.2 19.8 - - + +
372A ARG* 4.8 14.3 + - - +
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Residues in contact with GLN 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 ASP* 3.6 37.0 - - + +
56A ARG* 3.4 13.7 + - - +
57A ALA 3.2 0.4 - - - -
58A ALA* 1.3 78.1 - - + +
60A SER* 1.3 62.6 + - - +
62A LEU* 3.9 1.9 - - - +
63A ASN* 3.0 34.1 + - - +
392A VAL* 4.7 8.0 + - - +
395A ARG* 3.5 50.6 + - - +
396A GLY* 4.8 3.6 - - - -
397A ILE* 4.2 15.8 - - + +
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Residues in contact with SER 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 ARG 3.0 14.0 + - - -
57A ALA 3.0 7.6 + - - -
59A GLN* 1.3 77.1 - - - +
61A LEU* 1.3 60.4 + - - +
63A ASN* 3.5 6.9 + - - +
64A LYS* 3.2 26.0 + - - +
174A LEU* 4.0 9.3 - - - +
243A GLU* 3.3 31.2 + - - -
246A VAL* 4.1 15.2 - - - +
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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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57A ALA 2.9 12.0 + - - +
58A ALA* 3.6 9.2 - - - +
60A SER* 1.3 73.5 - - - +
62A LEU* 1.3 66.2 - - - +
64A LYS* 3.0 5.3 + - - +
65A LEU* 2.9 44.9 + - + +
171A THR* 5.9 0.2 - - - +
173A GLU* 3.5 41.7 - - + +
174A LEU* 3.7 12.8 - - + +
177A GLN* 3.7 29.6 - - + +
369A VAL* 4.2 20.4 - - + -
370A GLU* 4.9 4.3 - - - +
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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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58A ALA 2.9 17.8 + - - +
59A GLN* 3.9 4.3 - - - +
61A LEU* 1.3 71.9 - - - +
63A ASN* 1.3 63.6 + - - +
65A LEU* 3.2 2.4 + - + +
66A ILE* 3.2 30.1 + - + +
363A LEU* 5.8 1.1 - - + -
369A VAL* 3.6 20.7 - - + +
372A ARG* 4.0 28.7 - - + +
373A ALA* 3.7 39.5 - - + +
376A ILE* 4.0 17.0 - - + -
393A CYS 4.5 5.6 - - - +
397A ILE* 3.7 29.8 - - + -
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Residues in contact with ASN 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 GLN* 3.0 24.4 + - - +
60A SER* 3.8 7.5 - - - +
61A LEU 3.2 0.2 - - - -
62A LEU* 1.3 76.2 - - - +
64A LYS* 1.3 57.2 + - + +
66A ILE* 3.6 8.8 - - - +
67A ARG* 3.1 47.3 + - - +
140A SER* 4.5 10.7 + - - +
396A GLY 3.2 22.6 + - - -
397A ILE* 3.6 7.7 - - - +
398A ASP* 2.8 36.0 + - - +
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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 SER* 3.2 9.7 + - - +
61A LEU 3.0 9.4 + - - +
63A ASN* 1.3 73.5 - - + +
65A LEU* 1.3 66.1 + - - +
66A ILE 3.1 2.5 + - - -
67A ARG* 3.3 19.8 + - + +
140A SER* 6.5 0.9 - - - -
145A THR* 3.7 23.7 + - - +
174A LEU* 3.9 22.0 - - + -
177A GLN* 4.1 33.3 - - + +
178A THR* 5.8 2.7 - - - +
242A ASP* 5.1 2.0 - - - -
243A GLU* 3.1 25.6 - - - -
602A ADP 3.7 31.1 + - - +
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Residues in contact with LEU 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* 2.9 27.5 + - + +
62A LEU 3.2 4.7 + - - +
64A LYS* 1.3 77.2 - - - +
66A ILE* 1.3 59.9 + - - +
67A ARG 4.8 1.4 - - - +
177A GLN* 3.4 33.2 - - - +
369A VAL* 3.7 31.0 - - + +
370A GLU* 4.2 28.0 - - + +
373A ALA* 3.9 13.5 - - + -
377A GLU* 4.1 12.9 - - - +
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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* 3.2 21.1 + - + +
63A ASN* 3.6 11.7 - - - +
65A LEU* 1.3 79.3 - - - +
67A ARG* 1.3 68.6 + - - +
68A SER* 3.4 2.9 + - - -
373A ALA* 3.9 31.9 - - + +
376A ILE* 4.0 22.0 - - + -
377A GLU* 4.1 12.6 - - - +
380A ARG* 2.8 51.9 + - - +
397A ILE* 4.0 22.0 - - + -
398A ASP* 3.7 11.4 - - + +
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Residues in contact with ARG 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 ASN* 3.1 28.7 + - - +
64A LYS* 3.3 15.6 + - + +
65A LEU 4.8 1.6 - - - +
66A ILE* 1.3 77.2 - - - +
68A SER* 1.3 60.1 + - - +
69A ASN 3.2 23.9 + - - +
71A VAL* 4.2 18.8 - - - +
140A SER* 3.1 36.5 + - - -
141A GLY* 3.7 11.8 - - - -
380A ARG* 4.9 1.1 - - - +
398A ASP* 3.1 36.9 + - - +
400A GLU* 4.8 8.9 + - - -
602A ADP 3.9 26.8 + - - +
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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