Contacts of the helix formed by residues 84 - 96 (chain D) in PDB entry 3E8C
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 GLN 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D PHE* 3.8 36.5 - - + -
79D VAL* 2.8 23.3 + - + +
82D LEU* 2.8 31.4 + - + +
83D LYS* 1.3 82.5 + - - +
85D ILE* 1.3 59.3 + - - +
86D GLU 3.5 1.6 - - - -
87D HIS* 2.8 38.1 + - + +
88D THR* 2.9 31.0 + - - +
187D PHE* 3.9 14.3 - - - -
23J HIS* 5.3 9.9 - - - +
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Residues in contact with ILE 85 (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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79D VAL* 3.6 7.8 - - - +
80D VAL* 3.8 35.2 - - + +
83D LYS* 3.5 4.2 - - - -
84D GLN* 1.3 78.6 - - - +
86D GLU* 1.3 65.3 + - - +
88D THR* 3.2 3.3 + - - -
89D LEU* 3.1 35.0 + - + +
346D GLU* 3.6 49.6 - - + +
347D PHE* 4.0 15.8 - - + -
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Residues in contact with GLU 86 (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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84D GLN 3.5 0.2 - - - -
85D ILE* 1.3 79.1 - - - +
87D HIS* 1.3 60.3 + - + +
89D LEU* 3.2 13.7 + - + +
90D ASN* 2.8 47.4 + - - +
189D LYS* 3.9 26.0 + - - -
197D TPO 4.1 10.0 + - - -
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Residues in contact with HIS 87 (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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83D LYS 4.6 4.6 + - - -
84D GLN* 2.8 41.4 + - + +
85D ILE 3.2 0.8 - - - -
86D GLU* 1.3 81.1 - - + +
88D THR* 1.3 57.4 + - - +
90D ASN* 3.4 15.7 + - - +
91D GLU* 2.9 30.2 + - - +
165D ARG* 3.8 11.8 + - - -
186D GLY 3.3 22.3 - - - +
187D PHE* 3.9 16.5 - + - -
197D TPO 2.8 47.7 + - + +
199D CYS* 4.6 3.4 - - + -
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Residues in contact with THR 88 (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 PHE* 4.4 10.9 - - - -
74D LEU* 5.0 7.4 - - + +
79D VAL* 3.6 18.4 - - - +
84D GLN* 2.9 20.4 + - - +
85D ILE 3.4 5.2 - - - -
87D HIS* 1.3 76.1 - - - +
89D LEU* 1.3 62.9 + - + +
91D GLU* 3.5 16.3 + - - +
92D LYS* 3.2 22.9 + - - +
116D LEU* 3.4 33.4 - - + -
118D MET* 5.1 1.9 - - + +
347D PHE* 4.6 3.4 - - + -
350D PHE* 4.0 13.6 - - + -
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Residues in contact with LEU 89 (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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85D ILE* 3.1 34.7 + - + +
86D GLU* 3.2 12.8 + - + +
88D THR* 1.3 72.8 - - - +
90D ASN* 1.3 64.5 + - - +
92D LYS* 3.6 4.4 + - - +
93D ARG* 3.1 27.8 + - - +
346D GLU 4.2 9.4 - - - +
347D PHE* 4.6 12.3 - - + -
349D GLU* 3.8 44.7 - - + +
350D PHE* 4.1 28.0 - - + +
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Residues in contact with ASN 90 (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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30D TRP* 5.7 5.1 - - - -
86D GLU* 2.8 46.0 + - - +
87D HIS* 3.4 19.9 - - - +
89D LEU* 1.3 73.3 - - - +
91D GLU* 1.3 57.6 - - - +
93D ARG* 4.0 2.9 - - - +
94D ILE* 2.9 42.0 + - + +
188D ALA 3.2 24.0 + - - +
189D LYS* 4.2 20.6 - - - +
190D ARG 5.0 2.3 + - - -
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Residues in contact with GLU 91 (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 PHE* 6.0 1.2 - - - -
72D LYS* 2.7 29.3 + - - +
74D LEU* 5.5 1.2 - - - +
87D HIS 2.9 16.1 + - - +
88D THR* 3.5 14.5 + - - +
89D LEU 3.3 0.2 - - - -
90D ASN* 1.3 76.4 - - - +
92D LYS* 1.3 57.9 + - - +
94D ILE* 4.1 2.4 - - - +
95D LEU* 3.1 41.2 + - + +
118D MET* 3.4 23.4 - - - +
185D PHE* 3.3 26.4 - - - +
186D GLY* 3.7 15.5 + - - -
188D ALA 5.1 0.2 - - - -
351D G96 2.5 27.6 + - - +
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Residues in contact with LYS 92 (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 PRO* 5.3 6.6 - - - +
34D ALA 3.0 24.6 + - - +
35D GLN* 3.8 6.5 - - - +
88D THR 3.2 7.2 + - - +
89D LEU* 4.2 3.4 - - - +
91D GLU* 1.3 77.1 - - - +
93D ARG* 1.3 68.0 + - - +
95D LEU* 3.4 4.0 + - - +
96D GLN* 3.1 34.0 + - + +
106D LEU* 4.0 7.5 - - + +
109D SER* 3.6 23.8 + - - +
118D MET* 4.2 9.9 - - - -
349D GLU 4.0 4.7 + - - -
350D PHE* 2.7 76.3 + - + +
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Residues in contact with ARG 93 (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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30D TRP* 3.4 73.7 + - + +
31D GLU* 5.2 1.8 + - - +
33D PRO* 4.8 12.6 - - + +
89D LEU 3.1 19.6 + - - +
90D ASN* 4.0 2.7 - - - +
92D LYS* 1.3 81.2 - - - +
94D ILE* 1.3 62.3 + - - +
96D GLN* 2.8 36.7 + - - +
97D ALA* 3.6 5.2 - - - +
349D GLU* 4.8 15.3 + - - +
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Residues in contact with ILE 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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26D PHE* 5.1 0.7 - - + -
30D TRP* 3.8 22.4 - - + -
90D ASN* 2.9 22.3 + - + +
91D GLU 4.1 2.0 - - - +
93D ARG* 1.3 74.8 - - - +
95D LEU* 1.3 66.9 + - - +
97D ALA* 3.0 12.5 + - - +
98D VAL* 3.1 31.2 + - + +
162D LEU* 3.8 29.4 - - + -
185D PHE* 4.1 20.6 - - + -
188D ALA* 3.5 40.6 - - + +
189D LYS* 3.6 9.2 - - - +
190D ARG 4.1 1.3 - - - +
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Residues in contact with LEU 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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91D GLU* 3.1 31.6 + - + +
92D LYS 3.4 0.4 + - - +
94D ILE* 1.3 77.4 - - - +
96D GLN* 1.3 60.3 + - - +
97D ALA 3.4 0.7 + - - -
98D VAL* 3.4 26.4 + - + +
103D LEU* 6.1 0.4 - - + -
104D VAL 4.0 20.6 - - - +
105D LYS 5.6 0.2 - - - -
106D LEU* 3.8 37.9 + - + +
118D MET* 4.7 2.2 - - - -
185D PHE* 4.0 31.9 - - + -
351D G96 3.4 44.4 - - + +
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Residues in contact with GLN 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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29D LYS* 3.1 39.8 + - - +
30D TRP* 4.3 0.8 - - - +
32D ASN 4.5 0.5 - - - +
33D PRO* 3.3 34.6 - - + +
34D ALA* 3.5 18.7 + - + +
92D LYS* 3.1 27.0 + - + +
93D ARG* 2.8 26.9 + - - +
95D LEU* 1.3 75.6 - - - +
97D ALA* 1.3 64.5 + - - +
98D VAL 4.8 1.0 - - - +
106D LEU* 4.1 15.9 - - + +
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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