Contacts of the helix formed by residues 77 - 92 (chain D) in PDB entry 6CXI
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 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D LYS* 5.1 8.4 - - - +
69D PRO* 4.0 8.0 + - + +
75D VAL* 4.6 3.5 - - - +
76D THR* 1.3 86.4 + - - +
78D TRP* 1.3 67.5 + - - +
79D ASP* 3.4 21.7 + - - +
80D ASP* 3.3 42.4 + - + +
81D MET* 3.6 11.3 + - - +
205J GLN* 5.5 4.8 + - - -
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Residues in contact with TRP 78 (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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75D VAL* 3.3 40.6 + - + +
76D THR 5.4 1.6 - - - -
77D ASN* 1.3 76.3 + - - +
79D ASP* 1.3 69.9 + - - +
81D MET* 3.2 13.9 + - + +
82D GLU* 3.0 20.1 + - - +
85D TRP* 5.3 7.5 - + - -
113D ALA* 5.0 2.7 - - + -
114D ASN* 4.6 18.8 - - - -
117D LYS* 3.3 40.8 - - + +
118D MET* 4.4 17.7 - - + -
121D ILE* 3.2 37.6 - - + +
203J VAL 5.1 10.8 - - - -
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Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ASN* 3.4 15.9 + - - +
78D TRP* 1.3 77.3 - - - +
80D ASP* 1.3 67.9 + - - +
82D GLU* 3.1 15.0 + - - +
83D LYS* 3.0 29.4 + - - +
204J GLY* 5.7 2.9 - - - -
205J GLN* 3.7 35.7 + - - +
206J HIS* 4.7 15.3 + - - -
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Residues in contact with ASP 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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34D VAL* 4.3 24.0 - - + +
36D ARG* 4.5 10.6 + - - -
67D LYS* 4.4 19.6 - - - +
69D PRO* 4.0 16.8 - - + +
77D ASN* 3.3 36.0 + - - +
78D TRP 3.3 0.6 - - - -
79D ASP* 1.3 77.6 - - - +
81D MET* 1.3 62.6 + - - +
83D LYS* 3.2 26.2 + - - +
84D ILE* 3.1 26.8 + - - +
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Residues in contact with MET 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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11D ASN* 4.5 8.1 - - - +
32D SER* 5.2 1.8 - - - +
69D PRO* 4.0 14.5 - - + +
70D ILE* 3.5 39.3 - - + -
75D VAL* 3.7 15.5 - - + -
77D ASN 3.6 9.3 + - - +
78D TRP* 3.2 18.1 + - + +
80D ASP* 1.3 77.3 - - - +
82D GLU* 1.3 59.5 + - - +
84D ILE* 3.1 17.1 + - + +
85D TRP* 2.8 74.2 + - + +
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Residues in contact with GLU 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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78D TRP 3.0 12.4 + - - +
79D ASP* 3.1 18.6 + - - +
81D MET* 1.3 77.0 - - - +
83D LYS* 1.3 63.6 + - - +
85D TRP* 3.4 11.3 + - + +
86D HIS* 2.8 47.5 + - - +
121D ILE* 5.6 3.8 - - + -
125D THR* 3.8 29.7 - - + +
126D PHE* 4.4 6.7 - - + -
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Residues in contact with LYS 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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34D VAL* 4.8 11.7 - - + +
36D ARG* 4.5 15.8 - - - +
51D SER* 4.5 13.1 + - - -
53D VAL* 5.0 18.3 - - + +
79D ASP* 3.0 21.1 + - - +
80D ASP* 3.2 26.5 + - - +
82D GLU* 1.3 82.2 - - - +
84D ILE* 1.3 58.0 + - + +
86D HIS* 3.4 6.9 + - - +
87D HIS* 2.8 31.1 + - - +
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Residues in contact with ILE 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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16D CYS* 3.6 31.0 - - + -
30D PHE* 4.0 11.7 - - + -
32D SER* 3.4 30.3 - - - +
33D ILE* 5.1 1.6 - - - +
34D VAL* 5.7 5.8 - - + -
53D VAL* 5.5 9.0 - - + -
69D PRO* 3.4 33.0 - - + -
80D ASP* 3.1 14.3 + - + +
81D MET* 3.3 20.0 - - + +
83D LYS* 1.3 76.0 - - + +
85D TRP* 1.3 62.3 + - + +
87D HIS* 3.2 7.8 + - - +
88D THR* 2.8 32.9 + - - +
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Residues in contact with TRP 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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9D ILE* 3.9 24.1 - - + +
11D ASN* 3.3 37.7 + - - +
16D CYS* 4.8 3.8 - - - -
78D TRP* 5.3 6.1 - + - -
81D MET* 2.8 48.8 + - + +
82D GLU* 3.8 5.6 - - - +
84D ILE* 1.3 74.2 - - - +
86D HIS* 1.3 61.1 + - - +
88D THR* 2.8 20.5 + - - -
89D PHE* 2.8 23.3 + + + -
104D LEU* 4.2 11.4 - - + +
118D MET* 4.2 26.0 - - + -
121D ILE* 3.8 29.6 - - + -
122D MET* 3.7 23.8 - - + -
126D PHE* 3.6 22.2 - + + -
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Residues in contact with HIS 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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82D GLU* 2.8 33.4 + - - +
83D LYS* 3.5 7.9 + - - +
85D TRP* 1.3 75.7 - - - +
87D HIS* 1.3 65.2 + - - +
90D TYR* 3.1 72.4 + + + +
91D ASN* 5.1 3.9 + - - -
126D PHE* 4.1 10.9 - + + -
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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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30D PHE* 3.1 41.0 - + + -
53D VAL* 4.6 26.1 + - + -
54D GLY* 5.2 4.9 - - - -
83D LYS 2.8 18.4 + - - +
84D ILE* 3.4 8.3 - - - +
86D HIS* 1.3 80.0 + - - +
88D THR* 1.3 56.6 + - - +
91D ASN* 3.0 62.3 + - - +
92D GLU* 3.2 33.2 + - - +
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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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9D ILE* 3.8 15.6 - - - +
16D CYS* 3.5 22.7 - - - -
18D ALA* 3.6 21.0 - - + +
28D ALA* 4.9 1.1 - - - -
30D PHE* 3.3 27.1 - - + -
84D ILE 2.8 20.5 + - - +
85D TRP* 2.8 19.2 + - + -
87D HIS* 1.3 78.9 - - - +
89D PHE* 1.3 61.4 + - - +
92D GLU* 3.9 7.3 + - - +
93D LEU* 3.0 31.4 + - - +
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Residues in contact with PHE 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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7D LEU* 3.4 41.5 - - + -
9D ILE* 3.4 30.3 - - + -
85D TRP* 2.8 34.9 + + + +
88D THR* 1.3 81.3 + - - +
90D TYR* 1.3 69.9 + - + +
93D LEU* 3.5 9.4 - - + +
94D ARG 3.0 6.4 + - - -
95D VAL* 2.9 44.0 + - + +
97D PRO* 4.4 14.4 - - + -
102D VAL* 4.1 15.0 - - + -
122D MET* 5.0 6.1 - - + -
126D PHE* 3.8 29.8 - + + -
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Residues in contact with TYR 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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86D HIS* 3.1 62.4 + + + +
89D PHE* 1.3 89.0 - - + +
91D ASN* 1.3 69.8 + - - +
92D GLU 3.6 0.2 - - - -
94D ARG* 3.6 23.3 - - - +
95D VAL 4.7 7.9 - - - -
96D ALA* 5.7 0.7 - - + -
97D PRO* 4.2 20.4 - - + +
98D GLU* 5.3 2.3 + - - -
126D PHE* 5.0 7.2 - + - -
38P LYS* 4.8 11.0 - - - +
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Residues in contact with ASN 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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86D HIS* 4.6 4.5 + - - +
87D HIS* 3.0 55.5 + - + +
90D TYR* 1.3 78.1 - - - +
92D GLU* 1.3 72.9 + - - +
94D ARG* 4.2 14.7 + - - -
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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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27D ARG* 4.3 18.0 - - - +
28D ALA* 3.2 36.3 - - + +
29D VAL 5.6 0.2 - - - +
30D PHE* 4.7 3.6 - - - +
87D HIS* 3.2 46.9 + - - +
88D THR* 4.2 0.3 - - - -
91D ASN* 1.3 82.9 - - - +
93D LEU* 1.3 67.5 + - - +
94D ARG* 3.3 9.9 + - - +
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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