Contacts of the helix formed by residues 93 - 104 (chain D) in PDB entry 5IYB
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 HIS 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D LEU* 3.9 26.0 + - + +
22D PHE* 3.4 33.4 - + - -
27D GLU* 5.3 8.6 + - - -
92D LEU* 1.3 75.3 - - - +
94D LYS* 1.3 79.2 + - + +
95D PHE* 3.0 19.2 + - + +
96D GLU* 3.1 28.4 + - + +
97D LEU* 2.8 31.4 + - - +
121D ARG* 4.8 1.8 - - - +
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Residues in contact with LYS 94 (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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27D GLU 5.8 2.9 - - - +
28D THR* 4.3 11.6 + - - +
29D ALA 3.8 16.8 - - - +
30D GLU* 2.9 40.3 + - - +
31D THR* 3.3 31.5 + - + +
88D LEU* 6.1 7.4 - - + -
92D LEU 4.1 0.8 + - - -
93D HIS* 1.3 83.8 + - + +
95D PHE* 1.3 61.8 + - - +
97D LEU* 3.7 10.0 - - + +
98D ALA* 3.2 17.7 + - - +
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Residues in contact with PHE 95 (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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17D ALA* 3.6 31.2 - - + -
20D LEU* 4.4 4.0 - - + -
22D PHE* 3.5 27.8 - + + -
31D THR* 4.2 6.5 - - + +
93D HIS* 3.0 16.2 + - + +
94D LYS* 1.3 76.1 - - - +
96D GLU* 1.3 62.9 + - + +
98D ALA* 3.3 3.5 + - - +
99D CYS* 2.9 43.9 + - + +
115D ILE* 6.1 3.8 - - + -
1G MET* 4.3 17.3 - - + +
3G TYR* 4.2 10.1 - + - -
80G PHE* 3.5 25.1 - + - -
83G GLU* 3.5 40.4 - - + -
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Residues in contact with GLU 96 (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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20D LEU* 4.0 20.4 - - + +
92D LEU* 4.1 9.1 - - + +
93D HIS* 3.1 34.0 + - + +
95D PHE* 1.3 78.5 - - + +
97D LEU* 1.3 57.4 + - - +
99D CYS* 3.9 1.2 - - - +
100D LEU* 2.9 34.8 + - + +
115D ILE* 4.2 21.0 - - + +
117D SER* 2.2 42.4 + - - +
118D LEU* 3.8 22.5 - - + +
121D ARG* 4.2 12.9 + - - -
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Residues in contact with LEU 97 (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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31D THR* 4.6 0.2 - - - +
84D ARG* 3.3 38.8 - - - +
87D LEU* 3.8 53.1 - - + +
88D LEU* 3.8 13.9 - - + +
92D LEU* 4.7 19.2 - - + +
93D HIS 2.8 22.2 + - - +
94D LYS* 3.7 11.7 - - + +
96D GLU* 1.3 73.9 - - - +
98D ALA* 1.3 60.8 + - - +
100D LEU* 3.5 4.6 + - - +
101D ALA* 2.8 31.5 + - + +
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Residues in contact with ALA 98 (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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31D THR* 3.8 16.8 - - + +
32D LEU 4.4 7.4 - - - +
33D LEU* 5.6 1.0 - - - +
84D ARG* 5.3 1.6 - - - +
94D LYS 3.2 16.4 + - - +
95D PHE 3.8 1.8 - - - +
97D LEU* 1.3 81.7 - - + +
99D CYS* 1.3 53.1 + - - +
101D ALA* 3.4 7.5 - - - +
102D ASN* 2.6 44.8 + - - +
1G MET* 3.7 25.4 - - + -
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Residues in contact with CYS 99 (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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95D PHE* 2.9 27.2 + - + +
96D GLU 3.9 2.9 - - - +
98D ALA* 1.3 73.3 - - - +
100D LEU* 1.3 60.3 + - - +
102D ASN* 3.4 4.5 + - - +
103D LEU* 2.9 48.2 + - - +
115D ILE* 4.1 19.5 - - + -
1G MET* 4.0 11.4 - - + +
83G GLU* 4.4 17.3 - - - -
84G VAL* 3.9 25.1 - - - -
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Residues in contact with LEU 100 (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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87D LEU* 5.0 8.5 - - + -
92D LEU* 5.0 14.1 - - + -
96D GLU 2.9 19.6 + - - +
97D LEU* 3.6 5.6 - - - +
99D CYS* 1.3 77.2 - - - +
101D ALA* 1.3 58.2 + - - +
103D LEU* 4.9 1.3 - - - -
104D CYS* 3.0 24.1 + - - -
105D PRO* 3.1 32.3 - - + +
111D SER* 5.2 2.9 - - - +
115D ILE* 4.5 7.3 - - + +
118D LEU* 4.6 17.9 - - + -
127D LEU* 3.9 26.5 - - + -
130D ILE* 5.1 3.8 - - + -
131D LEU* 4.2 5.8 - - + -
134D ILE* 3.6 29.9 - - + +
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Residues in contact with ALA 101 (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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33D LEU* 4.6 25.5 - - + +
73D ARG* 4.7 4.7 - - - +
74D PHE* 6.0 3.4 - - + -
83D VAL* 5.9 3.4 - - + -
87D LEU* 4.8 11.9 - - + -
97D LEU* 2.8 20.8 + - + +
98D ALA* 3.4 10.5 - - - +
100D LEU* 1.3 81.0 - - - +
102D ASN* 1.3 60.8 + - - +
104D CYS* 3.3 21.3 - - - -
134D ILE* 5.7 3.1 - - - -
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Residues in contact with ASN 102 (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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32D LEU 4.3 5.5 + - - -
33D LEU* 4.5 2.8 - - - +
34D ASN* 3.3 43.2 + - - +
73D ARG* 3.9 21.9 + - - +
98D ALA* 2.6 32.8 + - - +
99D CYS* 3.7 6.7 - - - +
100D LEU 3.3 0.2 - - - -
101D ALA* 1.3 75.3 - - - +
103D LEU* 1.3 66.4 + - + +
1G MET* 3.6 26.3 - - - +
2G PHE* 5.4 2.2 - - - -
85G VAL* 6.6 0.4 - - + -
86G ASP* 4.1 5.1 - - - +
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Residues in contact with LEU 103 (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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73D ARG* 4.6 6.7 + - - -
99D CYS* 2.9 33.7 + - - +
100D LEU* 4.9 0.9 - - - -
102D ASN* 1.3 75.0 - - + +
104D CYS* 1.3 73.4 + - - +
105D PRO* 3.5 8.9 - - + +
114D LEU* 3.7 33.4 - - + -
115D ILE* 5.5 2.7 - - + -
138D ARG* 5.7 0.7 + - - -
84G VAL* 3.6 45.5 - - + +
85G VAL* 4.3 3.8 - - - -
86G ASP* 3.8 25.9 - - - +
144G ARG* 5.4 3.6 - - + -
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Residues in contact with CYS 104 (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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73D ARG* 4.1 32.3 - - - +
74D PHE* 5.4 7.0 - - - -
100D LEU 3.0 11.9 + - - -
101D ALA* 3.3 23.3 - - - -
102D ASN 3.3 1.0 - - - -
103D LEU* 1.3 79.7 - - - +
105D PRO* 1.3 71.2 - - - +
106D GLU* 3.9 1.2 + - - +
134D ILE* 4.4 21.1 - - + -
135D GLN* 3.6 8.8 + - - -
138D ARG* 3.6 31.1 + - - +
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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