Contacts of the helix formed by residues 86 - 99 (chain A) in PDB entry 3EDH
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 LYS 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.0 1.6 - - - -
84A CYS 3.8 0.6 - - - -
85A ASP* 1.3 88.3 + - - +
87A PHE* 1.3 68.0 + - - +
88A GLY 4.4 3.4 - - - +
89A ILE* 3.0 18.7 + - + +
90A VAL* 3.0 19.8 + - - +
215A DMS 6.0 7.1 - - + +
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Residues in contact with PHE 87 (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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29A VAL* 3.5 17.7 - - + +
32A GLN* 3.6 61.9 - - + +
33A ALA* 3.7 15.2 - - + +
36A HIS* 3.6 32.8 - + + -
86A LYS* 1.3 72.2 - - - +
88A GLY* 1.3 60.6 + - - +
90A VAL* 3.1 5.5 + - - +
91A VAL* 2.9 40.2 + - + +
180A THR* 3.3 26.7 - - - -
181A ARG* 4.7 1.1 - - + -
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Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 3.3 3.6 - - - +
87A PHE* 1.3 87.8 - - - +
89A ILE* 1.3 57.9 + - - +
91A VAL* 3.4 7.2 + - - +
92A HIS* 3.0 27.7 + - - +
146A ILE* 3.8 8.3 - - - +
176A ARG* 3.2 34.6 + - - -
180A THR 4.7 0.4 - - - -
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Residues in contact with ILE 89 (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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83A ASN 5.6 0.7 - - - +
84A CYS* 3.5 39.9 - - + +
86A LYS* 3.0 26.2 + - + +
88A GLY* 1.3 75.2 - - - +
90A VAL* 1.3 66.1 + - + +
92A HIS* 3.2 8.3 + - + +
93A GLU* 3.0 34.1 + - + +
176A ARG* 3.9 29.1 - - + +
214A DMS 6.1 2.9 - - + -
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Residues in contact with VAL 90 (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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29A VAL* 4.5 2.5 - - + -
30A PHE* 4.1 23.3 - - + -
33A ALA* 3.5 20.9 - - + -
57A PHE* 3.9 28.7 - - + -
77A ILE* 5.8 0.4 - - + -
79A ILE* 4.7 10.8 - - + -
84A CYS 4.9 1.3 - - - +
85A ASP* 3.7 20.4 - - - +
86A LYS 3.0 14.1 + - - +
87A PHE* 3.7 6.5 - - - +
89A ILE* 1.3 74.8 - - + +
91A VAL* 1.3 60.2 + - - +
93A GLU* 3.2 8.1 + - + +
94A LEU* 2.9 31.8 + - + +
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Residues in contact with VAL 91 (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 ALA* 3.8 21.1 - - + +
36A HIS* 3.9 14.1 - - + +
37A TRP* 3.1 27.2 + - - +
87A PHE* 2.9 49.7 + - + +
88A GLY* 3.7 7.9 - - - +
89A ILE 3.3 0.2 - - - -
90A VAL* 1.3 75.2 - - - +
92A HIS* 1.3 57.2 + - - +
94A LEU* 3.3 1.2 + - - -
95A GLY* 2.9 23.7 + - - -
146A ILE* 4.1 13.8 - - + +
181A ARG 5.0 0.2 - - - -
182A LEU* 3.8 21.3 - - + +
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Residues in contact with HIS 92 (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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88A GLY 3.0 13.6 + - - +
89A ILE* 3.3 11.7 - - + +
91A VAL* 1.3 76.1 - - - +
93A GLU* 1.3 66.9 + - - +
95A GLY* 2.9 16.6 + - - -
96A HIS* 3.1 11.2 + - - -
102A HIS* 3.6 14.8 - + - -
146A ILE* 2.7 33.9 + - + +
147A MET* 3.5 19.0 - - + +
176A ARG* 3.3 30.5 + - - +
210A ZN 2.0 37.5 - - - -
214A DMS 3.2 16.1 - - + +
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Residues in contact with GLU 93 (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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66A SER* 2.7 32.7 + - - +
77A ILE* 3.7 28.7 - - + -
78A SER 5.3 6.1 - - - +
79A ILE* 5.8 2.0 - - + -
89A ILE* 3.0 26.9 + - + +
90A VAL* 3.7 9.4 - - - +
92A HIS* 1.3 87.3 - - - +
94A LEU* 1.3 61.7 + - - +
96A HIS* 3.0 21.4 + - - +
97A VAL* 3.1 17.4 + - - +
214A DMS 2.9 36.3 - - - +
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Residues in contact with LEU 94 (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 ALA* 3.8 16.8 - - + +
34A MET* 3.8 36.3 - - + +
37A TRP* 3.5 22.7 - - + +
45A PHE* 3.9 16.6 - - + -
55A ILE* 3.8 28.9 - - + -
57A PHE* 4.1 5.8 - - + -
77A ILE* 3.8 14.4 - - + -
90A VAL* 2.9 24.4 + - + +
92A HIS 3.2 0.2 - - - -
93A GLU* 1.3 72.3 - - - +
95A GLY* 1.3 60.0 + - - +
97A VAL* 3.1 6.9 + - + +
98A VAL* 2.9 34.3 + - - +
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Residues in contact with GLY 95 (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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37A TRP* 3.4 24.1 - - - -
91A VAL 2.9 8.4 + - - -
92A HIS 2.9 9.5 + - - -
94A LEU* 1.3 75.9 - - - +
96A HIS* 1.3 61.9 + - - +
98A VAL 3.4 0.9 + - - -
99A GLY 3.3 5.7 + - - -
100A PHE* 2.9 26.3 + - - +
147A MET* 3.9 17.0 - - - -
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Residues in contact with HIS 96 (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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64A CYS* 5.2 1.7 - - - -
66A SER* 4.0 20.0 - - - -
67A TYR 3.8 6.1 - - - +
68A VAL* 3.2 16.7 - - + +
69A GLY 2.8 18.5 + - - -
92A HIS* 3.1 13.9 + + - -
93A GLU* 3.0 27.6 + - - +
95A GLY* 1.3 76.4 - - - +
97A VAL* 1.3 64.8 + - - +
99A GLY* 3.0 7.1 + - - -
100A PHE 2.8 23.6 + - - -
101A TRP* 4.3 2.0 - + - -
102A HIS* 3.3 22.7 - + - -
147A MET* 3.3 13.4 - - + +
210A ZN 2.1 36.4 - - - -
214A DMS 3.2 3.3 + - - -
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Residues in contact with VAL 97 (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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10A TRP* 2.9 34.0 + - + +
15A ILE* 4.0 17.3 - - + -
55A ILE* 3.6 33.0 - - + -
66A SER* 5.3 2.5 - - - -
67A TYR 4.1 9.0 - - - +
69A GLY* 3.1 13.4 - - - +
75A GLN* 4.7 4.9 - - - +
77A ILE* 3.8 30.5 - - + -
93A GLU 3.1 13.4 + - - +
94A LEU* 3.4 14.1 - - + +
96A HIS* 1.3 74.4 - - + +
98A VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 98 (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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3A THR* 5.2 0.2 - - - +
8A ARG 4.5 3.1 - - - +
9A VAL* 5.0 0.9 - - - -
10A TRP* 4.5 2.0 - - - -
15A ILE* 4.2 17.7 - - + -
37A TRP* 4.0 34.1 - - + -
43A VAL* 4.4 10.5 - - + -
45A PHE* 5.0 2.7 - - + -
69A GLY* 4.3 0.4 - - - -
94A LEU 2.9 20.3 + - - +
95A GLY 3.7 4.9 - - - +
97A VAL* 1.3 77.2 - - + +
99A GLY* 1.3 56.9 + - - +
100A PHE* 3.8 22.7 - - + -
190A ALA* 4.7 1.1 - - + -
193A LEU* 3.9 3.5 - - - +
194A TYR* 2.7 51.6 + - + -
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Residues in contact with GLY 99 (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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2A ALA* 3.7 1.4 - - - -
3A THR* 2.8 42.6 + - - +
68A VAL* 3.5 6.3 - - - +
69A GLY* 3.7 15.0 - - - -
95A GLY 3.3 0.8 + - - -
96A HIS 3.0 8.9 + - - -
98A VAL* 1.3 80.8 - - - +
100A PHE* 1.3 65.2 + - - +
193A LEU* 4.5 3.7 - - - +
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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