Contacts of the helix formed by residues 79 - 96 (chain D) in PDB entry 3EGC
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 ASN 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D ASP* 2.9 28.4 + - - +
77D ILE 3.5 4.1 - - - +
78D GLU* 1.3 76.2 - - - +
80D VAL* 1.3 64.3 + - - +
81D PHE* 3.0 19.5 + - - +
82D PHE* 3.1 29.2 + - + -
83D ALA 3.2 9.4 + - - -
253D SER* 5.8 2.6 + - - -
254D HIS* 2.7 35.2 + - - -
255D ARG* 3.9 24.2 - - - +
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Residues in contact with VAL 80 (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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78C GLU 3.4 26.2 - - - +
80C VAL* 3.9 22.2 - - + +
255C ARG* 5.5 2.9 - - - +
78D GLU 3.6 3.8 + - - -
79D ASN* 1.3 74.6 + - - +
81D PHE* 1.3 64.2 + - - +
83D ALA* 3.9 7.0 - - + -
84D GLU* 3.2 42.0 + - - +
254D HIS* 4.2 15.2 + - + +
255D ARG* 4.6 0.2 - - - +
283D LEU* 4.0 33.2 - - + -
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Residues in contact with PHE 81 (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 ASN* 3.0 19.5 + - - +
80D VAL* 1.3 82.1 - - - +
82D PHE* 1.3 96.1 + + - +
84D GLU* 3.4 3.7 + - - +
85D VAL* 3.1 42.3 + - + +
152D VAL* 6.0 0.4 - - + -
153D ASN* 3.8 30.3 - - + -
254D HIS* 4.8 4.3 - - + +
281D ASP* 4.1 11.0 - - - +
298D GLN* 3.6 34.5 - - + -
300D THR* 3.5 28.7 - - + +
303D ILE* 4.4 11.2 - - + -
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Residues in contact with PHE 82 (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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74D VAL* 3.6 22.0 - - + +
75D SER* 3.2 24.2 - - - -
76D ASP* 3.4 36.3 - - + +
77D ILE* 4.3 3.7 - - - +
79D ASN* 3.1 21.0 + - + -
81D PHE* 1.3 99.0 - + - +
83D ALA* 1.3 60.7 + - - +
85D VAL* 3.1 8.6 + - + +
86D ALA* 2.9 30.8 + - - +
107D GLU* 4.8 5.6 - - - -
130D ALA* 3.7 23.6 - - + -
152D VAL* 5.5 1.3 - - + -
153D ASN* 3.6 22.0 - - + -
154D ARG* 4.9 3.6 - - - -
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Residues in contact with ALA 83 (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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77C ILE* 3.5 39.2 - - - +
78C GLU* 4.3 4.7 - - - -
83C ALA* 4.2 5.6 - - + -
77D ILE* 3.8 25.4 + - + +
79D ASN 3.2 11.5 + - - +
80D VAL* 3.7 15.5 - - + +
81D PHE 3.4 0.2 - - - -
82D PHE* 1.3 77.7 - - - +
84D GLU* 1.3 56.1 + - - +
86D ALA* 3.6 1.6 + - - +
87D SER 3.1 19.6 + - - -
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Residues in contact with GLU 84 (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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78C GLU* 3.8 30.4 - - + +
80D VAL* 3.2 33.0 + - - +
81D PHE* 3.8 0.4 - - - +
83D ALA* 1.3 76.2 - - - +
85D VAL* 1.4 64.2 + - - +
87D SER* 3.3 3.8 + - - -
88D GLY 3.2 18.0 + - - -
300D THR* 2.5 44.2 + - - +
301D ARG* 3.5 34.0 + - + +
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Residues in contact with VAL 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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72D LEU* 5.4 4.7 - - + -
74D VAL* 5.6 4.0 - - + -
81D PHE* 3.1 45.8 + - + +
82D PHE* 3.1 11.4 + - + +
84D GLU* 1.4 74.4 - - - +
86D ALA* 1.3 60.5 + - - +
88D GLY 3.2 1.9 + - - -
89D VAL* 2.9 34.6 + - + +
152D VAL* 4.3 23.1 - - + -
300D THR* 3.6 23.3 - - - +
303D ILE* 4.0 12.1 - - + -
304D GLY* 3.3 16.7 - - - +
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Residues in contact with ALA 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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77C ILE* 5.0 2.9 - - + -
102C LEU* 4.6 11.0 - - + +
72D LEU* 3.7 30.3 - - + +
74D VAL* 5.1 2.0 - - + +
77D ILE* 4.2 17.3 - - + -
82D PHE 2.9 16.4 + - - +
83D ALA 3.6 6.3 - - - +
85D VAL* 1.3 78.8 - - - +
87D SER* 1.3 58.5 + - - +
89D VAL* 3.6 3.4 - - - +
90D GLU* 2.8 32.2 + - - +
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Residues in contact with SER 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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77C ILE* 3.8 12.5 - - - +
78C GLU* 2.8 32.4 + - - -
104C ASN* 3.5 15.7 + - - +
83D ALA 3.1 15.7 + - - -
84D GLU 3.3 10.5 - - - -
86D ALA* 1.3 75.9 - - - +
88D GLY* 1.3 56.8 + - - +
90D GLU* 3.3 6.3 + - - +
91D SER* 2.9 31.8 + - - -
301D ARG* 4.4 1.9 - - - +
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Residues in contact with GLY 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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84D GLU 3.2 8.5 + - - -
85D VAL 3.2 1.3 + - - -
87D SER* 1.3 79.2 + - - +
89D VAL* 1.3 62.5 + - - +
91D SER* 3.3 5.1 + - - -
92D GLU* 3.0 25.3 + - - +
301D ARG* 3.4 28.6 - - - +
305D GLN* 3.6 12.9 - - - +
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Residues in contact with VAL 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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72D LEU* 4.3 22.2 - - + -
85D VAL* 2.9 31.8 + - + +
86D ALA* 3.6 10.8 - - - +
88D GLY* 1.3 73.8 - - - +
90D GLU* 1.3 58.9 + - - +
93D ALA* 3.0 27.0 + - - +
100D VAL* 4.6 7.2 - - + -
128D ILE* 3.7 18.8 - - + -
304D GLY* 3.4 26.3 - - - +
308D MET* 2.8 35.5 - - + +
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Residues in contact with GLU 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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102C LEU* 3.7 28.0 - - + +
103C ALA* 3.2 12.7 - - - +
104C ASN* 2.9 47.1 + - + +
111C ARG* 4.5 2.6 + - - -
86D ALA 2.8 22.1 + - - +
87D SER* 3.8 5.4 - - - +
89D VAL* 1.3 71.7 - - - +
91D SER* 1.3 75.1 + - - +
93D ALA* 3.9 0.3 - - - +
94D ARG* 3.1 45.3 + - - +
100D VAL* 4.4 16.8 - - + -
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Residues in contact with SER 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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111C ARG* 5.5 9.0 + - - -
87D SER* 2.9 19.1 + - - -
88D GLY* 3.9 5.8 - - - -
90D GLU* 1.3 87.3 + - - +
92D GLU* 1.3 59.5 + - - +
94D ARG* 3.7 5.3 + - - +
95D HIS* 3.2 23.6 + - - +
305D GLN* 6.0 0.4 + - - -
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Residues in contact with GLU 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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88D GLY 3.0 16.8 + - - +
91D SER* 1.3 78.7 - - - +
93D ALA* 1.3 61.0 + - - +
95D HIS* 3.5 14.9 + - - +
96D LYS* 2.7 58.8 + - - +
305D GLN* 3.3 41.1 + - + +
308D MET* 3.7 22.7 - - + -
309D ARG* 3.5 23.9 + - + +
312D ILE* 4.5 1.1 - - + -
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Residues in contact with ALA 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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89D VAL 3.0 17.7 + - - +
90D GLU 3.9 1.8 - - - +
92D GLU* 1.3 73.8 - - - +
94D ARG* 1.3 58.6 + - - +
96D LYS* 3.0 4.3 + - - +
97D GLY 2.9 10.4 + - - -
98D TYR* 2.7 45.8 + - + +
100D VAL* 3.6 26.9 - - + -
308D MET* 3.7 17.0 - - + +
312D ILE* 4.7 3.1 - - - -
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Residues in contact with ARG 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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103C ALA* 5.0 1.0 - - - +
104C ASN 3.3 26.1 + - - +
105C THR* 4.2 1.2 - - - +
111C ARG* 2.5 62.3 + - - +
114C GLU* 3.7 11.5 + - - +
115C ALA* 3.1 27.7 - - - +
118C GLN* 4.5 21.1 + - - +
90D GLU* 3.1 33.5 + - - +
91D SER* 3.8 5.8 - - - +
93D ALA* 1.3 79.1 - - - +
95D HIS* 1.3 62.0 + - - +
97D GLY* 3.0 12.6 + - - +
98D TYR 3.6 7.5 + - - +
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Residues in contact with HIS 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 SER 3.2 16.4 + - - +
92D GLU* 3.6 17.7 + - - +
93D ALA 3.3 0.2 - - - -
94D ARG* 1.3 78.5 - - - +
96D LYS* 1.3 77.4 + - + +
97D GLY 3.9 0.2 + - - -
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Residues in contact with LYS 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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68D ASN* 4.5 2.3 + - - -
92D GLU* 2.7 43.4 + - - +
93D ALA 3.0 6.9 + - - +
95D HIS* 1.3 92.2 - - + +
97D GLY* 1.3 62.3 + - - +
98D TYR* 3.6 15.1 - - + -
309D ARG* 4.0 15.8 + - - +
312D ILE* 3.7 39.7 - - + +
313D HIS* 5.5 7.9 + - - -
316D GLU* 5.4 2.1 - - - +
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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