Contacts of the helix formed by residues 50 - 64 (chain D) in PDB entry 3ER8
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 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D ASN* 2.9 16.8 + - - +
49D LYS* 1.3 80.3 - - - +
51D ILE* 1.3 55.1 - - - +
52D PHE 2.6 4.9 - - - -
53D VAL* 2.5 36.7 + - - +
54D SER* 2.8 9.7 + - - -
75D LYS* 5.9 5.4 + - - -
79D LEU* 5.3 4.7 - - - +
600E C 3.1 59.7 + - + +
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Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D ASN* 3.1 20.7 + - + +
50D ASP* 1.3 74.8 - - - +
52D PHE* 1.3 62.0 + - - +
54D SER* 3.0 13.5 - - - -
55D LEU* 2.9 41.2 + - + -
600E C 4.4 8.4 + - - +
601E C 3.8 33.4 - - - +
602E U 4.2 11.7 - - + +
603E U 2.9 65.1 - - + +
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Residues in contact with PHE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 4.1 15.3 - + + -
48D ASN 4.0 11.0 - - - +
49D LYS* 4.2 10.5 - - - +
50D ASP* 2.6 1.0 - - - +
51D ILE* 1.3 79.9 - - - +
53D VAL* 1.3 57.5 + - - +
55D LEU* 2.8 21.5 + - - +
56D VAL* 3.1 25.9 + - + +
78D ILE* 3.9 12.3 - - + -
82D PHE* 3.6 25.6 - + - -
104D LEU* 4.0 31.2 - - + -
108D TYR* 3.4 44.0 - + + -
223D PHE* 3.6 22.7 - + - -
603E U 3.3 19.2 + - - +
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Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LYS 3.5 20.9 - - - +
50D ASP* 2.5 26.9 + - - +
52D PHE* 1.3 72.5 - - - +
54D SER* 1.3 55.0 + - - -
56D VAL 3.8 0.3 + - - -
57D LYS* 3.0 49.7 + - - +
74D ILE 3.6 3.0 - - - +
75D LYS* 3.3 41.3 - - + +
78D ILE* 3.7 28.0 - - + -
79D LEU* 4.2 11.0 - - + -
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Residues in contact with SER 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ASP* 2.8 5.2 + - - -
51D ILE* 3.0 23.7 - - - -
53D VAL* 1.3 79.1 - - - +
55D LEU* 1.3 57.1 + - - +
57D LYS* 4.0 5.7 - - - +
58D LYS* 3.1 27.0 + - - +
600E C 3.3 23.6 - - - -
601E C 3.6 38.8 + - - -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE* 2.9 37.3 + - + +
52D PHE* 2.8 9.8 + - - +
54D SER* 1.3 82.6 - - - +
56D VAL* 1.3 64.5 + - - +
57D LYS 3.1 1.8 - - - -
58D LYS* 3.2 25.6 + - + +
59D ASN* 3.4 6.2 - - - +
108D TYR* 3.6 33.2 + - + -
109D THR* 4.9 4.3 - - - +
113D GLY* 4.9 3.4 - - - -
601E C 4.3 7.2 - - + +
602E U 3.1 57.4 - - + +
603E U 4.5 4.3 - - + +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D PHE* 3.1 29.8 + - + +
53D VAL 4.4 0.4 - - - +
55D LEU* 1.3 76.2 - - - +
57D LYS* 1.3 58.8 + - - +
59D ASN* 3.3 4.9 - - - +
60D LYS* 3.1 21.5 + - - +
74D ILE* 3.5 19.3 - - + -
78D ILE* 3.4 28.5 - - + -
108D TYR* 3.9 14.1 - - + +
220D LEU* 4.0 11.0 - - + -
223D PHE* 3.7 21.5 - - + -
224D ILE* 3.6 19.6 - - + +
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D VAL* 3.0 41.5 + - + +
54D SER* 4.0 5.6 - - - +
55D LEU 3.1 0.2 - - - -
56D VAL* 1.3 74.4 - - - +
58D LYS* 1.3 53.6 + - - +
59D ASN 2.6 16.7 + - - -
60D LYS* 3.1 16.1 + - - +
61D LYS* 3.3 17.3 + - - +
71D ALA* 2.7 47.9 + - + +
74D ILE* 3.6 17.3 - - + +
75D LYS* 3.7 12.9 - - - +
601E C 6.3 0.4 - - - +
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D SER 3.1 18.3 + - - +
55D LEU* 3.2 10.6 + - + +
57D LYS* 1.3 75.2 - - - +
59D ASN* 1.3 57.7 + - - +
61D LYS* 2.8 30.8 + - - +
62D ARG* 5.9 0.8 - - - +
116D THR* 2.9 57.6 + - - +
601E C 2.8 49.4 - - + +
602E U 3.7 15.9 - - + +
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Residues in contact with ASN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU 3.4 8.3 - - - +
56D VAL* 3.3 12.3 - - - +
57D LYS 2.6 7.3 + - - -
58D LYS* 1.3 75.0 - - - +
60D LYS* 1.3 57.2 + - - +
61D LYS* 3.0 5.5 - - - +
62D ARG* 2.7 7.2 + - - -
63D PHE* 2.7 55.3 + - - -
64D PHE* 3.4 11.7 + - - -
108D TYR* 4.4 6.1 - - - +
112D LEU* 5.0 3.4 - - - +
115D LEU* 4.7 6.8 - - - +
116D THR* 4.7 1.8 - - - +
171D LEU* 4.6 4.0 - - - +
220D LEU* 3.1 43.8 - - - +
224D ILE* 3.5 9.3 - - - +
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Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL 3.1 11.5 + - - +
57D LYS* 3.1 12.5 + - - +
59D ASN* 1.3 77.4 - - - +
61D LYS* 1.3 61.6 + - + +
64D PHE* 2.4 63.8 + - - +
65D SER* 2.7 25.1 + - - +
67D VAL* 3.3 30.2 + - + -
69D THR 4.7 7.5 + - - -
74D ILE* 4.7 11.0 - - + -
224D ILE* 3.6 24.9 - - + +
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Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LYS 3.4 11.0 - - - +
58D LYS* 2.8 56.4 + - - +
59D ASN 3.0 0.8 - - - -
60D LYS* 1.3 86.1 - - + +
62D ARG* 1.3 88.1 + - + +
65D SER* 3.7 18.6 + - - +
601E C 6.1 0.7 - - - +
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS* 5.9 0.9 - - - +
59D ASN* 2.7 15.2 + - - +
61D LYS* 1.3 104.8 - - + +
63D PHE* 1.3 95.5 + - + +
65D SER* 5.3 2.2 - - - -
115D LEU 3.8 7.1 + - - -
116D THR* 3.8 20.9 - - + +
117D ILE 6.0 0.2 - - - +
174D GLU* 4.3 13.5 + - - +
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Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASN* 2.7 30.0 + - - -
62D ARG* 1.3 106.8 - - + +
64D PHE* 1.3 82.0 + - + +
65D SER 3.8 2.5 - - - -
66D ASP* 4.9 0.3 - - - +
115D LEU* 3.4 33.7 - - + -
116D THR* 4.3 1.1 - - + -
167D ASN* 3.2 23.9 - - - +
170D LYS* 3.8 20.8 - - + +
171D LEU* 3.4 33.2 - - + +
174D GLU* 3.6 30.3 - - + -
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASN* 3.7 21.8 - - - -
60D LYS* 2.4 44.7 + - - +
63D PHE* 1.3 93.6 - - + +
65D SER* 1.3 64.3 + - - +
66D ASP* 3.5 2.2 - - - -
67D VAL* 3.2 15.9 - - + +
164D LEU* 4.3 8.7 - - + -
167D ASN* 3.0 39.9 - - - -
168D VAL* 4.6 9.0 - - + -
171D LEU* 3.3 36.3 - - + -
220D LEU* 4.1 8.1 - - + -
221D ILE* 4.9 12.8 - - + -
224D ILE* 3.7 24.7 - - + -
225D THR* 5.2 0.7 - - - -
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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