Contacts of the helix formed by residues 58 - 71 (chain D) in PDB entry 5IY8
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 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D GLU 3.7 2.1 + - - -
57D LEU* 1.3 79.7 - - - +
59D GLU* 1.3 58.2 + - - +
60D VAL* 3.4 14.6 - - - +
61D PHE* 2.6 31.2 + - - +
62D MET* 2.9 27.9 + - - +
36G GLY* 4.4 16.6 - - - -
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Residues in contact with GLU 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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57D LEU 3.9 0.2 + - - -
58D SER* 1.3 69.6 - - - +
60D VAL* 1.3 57.8 + - + +
62D MET* 3.2 8.7 + - + +
63D LYS* 2.7 70.9 + - + +
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Residues in contact with VAL 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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58D SER* 3.4 11.2 - - - +
59D GLU* 1.3 77.5 - - + +
61D PHE* 1.3 58.3 + - - +
63D LYS* 4.5 2.0 - - + +
64D THR* 2.4 36.7 + - - +
36G GLY* 4.6 21.8 - - - +
44G PHE* 5.4 10.3 - - + -
45G VAL 6.0 1.1 - - - +
46G ILE* 5.4 9.4 - - + -
103G PRO* 3.5 37.2 - - + +
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Residues in contact with PHE 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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41D LEU* 3.2 59.0 - - + -
44D ARG* 4.2 10.5 - - + -
45D LYS* 3.9 11.2 - - + -
57D LEU* 3.4 42.4 - - + -
58D SER* 2.6 31.6 + - - +
60D VAL* 1.3 73.1 - - - +
62D MET* 1.3 66.0 + - - +
64D THR* 2.8 11.0 + - - -
65D LEU* 2.7 49.9 + - + +
46G ILE* 5.2 10.5 - - + +
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Residues in contact with MET 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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45D LYS* 5.1 16.4 - - + +
56D GLU* 6.4 0.9 - - + -
57D LEU* 4.5 19.1 - - + +
58D SER 2.9 20.3 + - - +
59D GLU* 3.5 10.8 - - + +
61D PHE* 1.3 92.2 - - + +
63D LYS* 1.3 58.5 + - + +
65D LEU* 3.3 14.8 + - - +
66D ASN* 2.9 29.9 + - - +
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Residues in contact with LYS 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 GLU* 2.7 56.2 + - + +
60D VAL* 3.9 4.3 - - + +
62D MET* 1.3 73.6 - - + +
64D THR* 1.3 57.9 + - - +
66D ASN* 3.4 5.5 + - - +
67D TYR* 3.0 30.8 + - - +
100G GLU* 3.4 29.9 + - - +
102G GLY* 3.7 24.1 - - - +
103G PRO* 4.2 12.8 - - + +
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Residues in contact with THR 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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37D VAL* 5.3 0.9 - - + -
41D LEU* 3.9 18.4 - - + -
60D VAL* 2.4 28.1 + - - +
61D PHE* 2.8 10.1 + - - -
63D LYS* 1.3 70.7 - - - +
65D LEU* 1.3 65.8 + - - +
67D TYR* 4.2 2.0 - - + +
68D THR* 3.1 30.1 + - - +
2G PHE* 4.3 25.4 - - + -
46G ILE* 4.3 18.3 - - + +
102G GLY* 4.3 8.5 - - - -
103G PRO* 3.2 23.4 - - + +
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Residues in contact with LEU 65 (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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38D HIS* 4.0 18.4 - - + +
41D LEU* 3.7 30.2 - - + +
42D GLU* 3.8 17.0 - - + +
45D LYS* 4.3 22.7 - - + +
61D PHE* 2.7 34.6 + - + +
62D MET* 3.5 17.3 - - - +
64D THR* 1.3 73.2 - - - +
66D ASN* 1.3 57.3 + - - +
68D THR* 3.3 6.1 - - + +
69D ALA* 3.1 30.9 + - + +
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Residues in contact with ASN 66 (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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62D MET 2.9 16.7 + - - +
63D LYS* 3.7 6.7 - - - +
64D THR 3.3 0.2 - - - -
65D LEU* 1.3 76.4 - - - +
67D TYR* 1.3 66.0 + - - +
69D ALA* 3.7 2.3 - - - +
70D ARG* 2.9 29.6 + - - +
142D TYR* 3.2 26.3 + - - -
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Residues in contact with TYR 67 (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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34D ASN* 4.6 14.0 + - - -
63D LYS 3.0 17.4 + - - +
64D THR* 4.2 4.0 - - + +
66D ASN* 1.3 74.7 - - - +
68D THR* 1.3 81.3 + - - +
70D ARG* 3.2 10.1 + - - +
71D PHE* 3.0 55.9 + + - +
2G PHE* 4.4 25.5 - + - -
77G PHE* 6.2 0.4 - + - -
85G VAL* 5.6 1.2 - - - +
86G ASP* 3.4 25.5 + - - +
88G VAL* 5.0 8.5 - - + -
100G GLU 4.8 4.0 - - - -
101G ILE* 3.9 23.4 - - + +
102G GLY* 3.6 26.2 - - - +
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Residues in contact with THR 68 (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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34D ASN* 3.0 38.2 + - - +
37D VAL* 4.3 9.4 - - - +
38D HIS* 3.6 31.7 + - + +
41D LEU* 4.5 4.7 - - + -
64D THR* 3.1 22.5 + - - +
65D LEU* 3.3 11.9 - - - +
67D TYR* 1.3 88.9 - - - +
69D ALA* 1.3 67.0 + - - +
71D PHE* 3.2 5.6 + - - +
72D SER* 3.1 20.3 + - - -
2G PHE* 4.4 3.4 - - - -
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Residues in contact with ALA 69 (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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38D HIS* 3.7 29.6 - - + +
65D LEU* 3.1 16.3 + - + +
66D ASN* 3.7 4.0 - - - +
68D THR* 1.3 82.1 - - - +
70D ARG* 1.3 62.6 + - - +
71D PHE 3.0 1.4 + - - -
72D SER* 3.1 17.2 + - - -
141D GLN* 5.4 0.3 + - - -
142D TYR* 3.3 31.9 - - + +
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Residues in contact with ARG 70 (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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66D ASN* 2.9 24.7 + - - +
67D TYR* 3.2 8.7 + - - +
69D ALA* 1.3 74.9 - - - +
71D PHE* 1.3 73.4 + - + +
72D SER 3.5 0.9 + - - -
140D PHE* 4.0 15.1 - - - -
142D TYR* 3.4 37.3 + - + -
88G VAL* 3.6 20.0 - - - +
140G ASP* 2.5 56.0 + - - -
142G GLU* 2.4 45.1 + - - +
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Residues in contact with PHE 71 (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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34D ASN* 3.8 21.4 + - - +
67D TYR* 3.0 51.6 + + + +
68D THR* 3.4 6.5 - - - +
69D ALA 3.1 0.4 - - - -
70D ARG* 1.3 90.5 - - + +
72D SER* 1.3 65.8 + - - +
73D ARG* 3.5 32.4 + - - +
86G ASP* 3.5 35.2 - - + -
87G ALA 4.3 2.9 - - - -
88G VAL* 4.3 11.7 - - + -
142G GLU* 3.2 51.1 - - + -
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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