Contacts of the helix formed by residues 83 - 98 (chain D) in PDB entry 6GYS
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 ARG 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D GLU* 3.1 28.7 - - + +
81D ASN 3.3 7.8 + - - +
82D VAL* 1.3 74.5 - - - +
84D SER* 1.3 59.3 + - - +
85D SER* 3.2 3.6 - - - +
86D VAL* 3.0 12.4 + - + +
87D LEU 2.9 22.7 + - - -
129D GLU* 4.0 15.6 + - - -
130D MET* 4.4 7.3 - - - +
133D GLU* 2.2 50.0 + - - +
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Residues in contact with SER 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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10D SER* 2.4 31.4 + - - -
12D GLU* 2.6 26.5 + - - +
14D GLU* 3.2 32.5 - - - +
16D PHE* 3.2 20.0 - - - -
82D VAL 3.7 0.2 + - - -
83D ARG* 1.3 72.3 - - - +
85D SER* 1.3 56.2 + - - +
87D LEU* 3.7 9.4 - - - -
88D GLN* 2.8 23.4 + - - +
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLU* 4.4 1.0 + - - -
83D ARG* 3.2 2.5 + - - +
84D SER* 1.3 79.1 - - - +
86D VAL* 1.3 62.0 + - - +
88D GLN* 3.1 9.5 + - - +
89D LYS* 2.9 32.7 + - - +
130D MET* 6.1 0.7 - - - +
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Residues in contact with VAL 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 VAL* 4.2 7.9 - - + -
83D ARG* 3.0 12.0 + - + +
85D SER* 1.3 77.2 - - - +
87D LEU* 1.3 60.2 + - - +
89D LYS* 3.1 11.0 + - + +
90D VAL* 2.9 30.9 + - + +
130D MET* 3.7 19.5 - - + -
133D GLU* 3.5 37.7 - - + +
134D ILE* 3.6 42.8 - - + +
137D ALA* 4.8 2.2 - - + -
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Residues in contact with LEU 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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8D LEU* 3.7 38.1 - - + -
10D SER* 4.0 24.5 - - - +
16D PHE* 3.7 23.6 - - + -
79D VAL* 5.1 8.5 - - + -
82D VAL* 3.6 23.2 - - + +
83D ARG 2.9 8.7 + - - +
84D SER* 3.6 9.6 - - - +
85D SER 3.3 0.2 - - - -
86D VAL* 1.3 76.0 - - - +
88D GLN* 1.3 56.1 + - - +
90D VAL* 3.1 14.5 + - + +
91D ILE* 2.9 30.8 + - - +
137D ALA* 6.1 0.2 - - + -
141D LEU* 4.5 19.5 - - + -
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Residues in contact with GLN 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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16D PHE* 4.0 19.5 - - + +
84D SER 2.8 16.0 + - - +
85D SER* 3.1 13.0 + - - +
87D LEU* 1.3 74.5 - - - +
89D LYS* 1.3 59.5 + - + +
91D ILE* 3.1 28.4 + - - +
92D GLU* 2.9 60.9 + - - +
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Residues in contact with LYS 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 SER* 2.9 23.1 + - - +
86D VAL* 3.1 15.9 + - + +
88D GLN* 1.3 76.0 - - + +
90D VAL* 1.3 56.8 + - + +
92D GLU* 3.3 15.6 + - - +
93D TRP* 2.9 23.6 + - - +
123D PHE* 3.0 66.1 + - + +
124D LEU* 4.7 4.5 - - + -
126D VAL* 4.7 14.0 - - - +
130D MET* 5.4 11.2 - - + -
134D ILE* 5.3 8.5 - - + -
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Residues in contact with VAL 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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8D LEU* 6.0 1.1 - - + -
86D VAL* 2.9 21.4 + - + +
87D LEU* 3.1 22.0 + - + +
89D LYS* 1.3 76.2 - - + +
91D ILE* 1.3 64.3 + - + +
93D TRP* 3.2 10.1 + - - +
94D ALA* 3.0 22.1 + - + +
134D ILE* 5.1 9.4 - - + +
137D ALA* 4.2 22.4 - - + -
138D ALA 5.5 0.4 - - - +
141D LEU* 4.8 3.6 - - + -
143D ILE* 3.7 30.3 - - + -
146D LEU* 4.0 16.2 - - + -
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Residues in contact with ILE 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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8D LEU* 3.7 25.6 - - + -
16D PHE* 3.7 37.2 - - + -
18D VAL* 3.8 23.8 - - + -
22D ILE* 5.0 4.9 - - + -
87D LEU* 2.9 19.5 + - + +
88D GLN* 3.1 25.8 + - - +
90D VAL* 1.3 76.0 - - + +
92D GLU* 1.3 58.0 + - - +
94D ALA* 3.1 9.5 + - - +
95D GLU* 2.8 43.5 + - + +
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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 GLN* 2.9 45.6 + - - +
89D LYS* 3.5 25.7 + - - +
90D VAL 3.2 0.2 - - - -
91D ILE* 1.3 73.2 - - - +
93D TRP* 1.3 61.8 + - - +
95D GLU* 3.1 13.6 + - + +
96D HIS* 3.0 27.0 + - - +
119D TRP* 4.6 3.1 + - + -
123D PHE* 3.6 23.1 - - + -
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Residues in contact with TRP 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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25D ARG* 3.2 44.4 - - - -
89D LYS 2.9 9.4 + - - +
90D VAL* 3.4 11.0 - - - +
92D GLU* 1.3 77.3 - - - +
94D ALA* 1.3 62.1 + - + +
96D HIS* 3.3 1.6 + - - -
97D HIS* 2.9 59.3 + + + +
102D PHE* 3.6 13.2 - + - -
119D TRP* 4.9 0.2 - + - -
120D ASP* 2.7 37.4 + - + -
123D PHE* 3.3 26.6 - + + -
124D LEU* 5.1 1.3 - - + -
143D ILE* 4.1 4.0 - - + -
145D PRO* 4.1 4.3 - - + -
146D LEU* 3.4 61.1 - - + +
149D ALA* 4.6 3.1 - - + +
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Residues in contact with ALA 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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22D ILE* 3.7 24.5 - - + +
25D ARG* 4.1 22.2 - - + -
90D VAL* 3.0 14.0 + - + +
91D ILE* 3.1 11.0 + - - +
93D TRP* 1.3 84.8 - - + +
95D GLU* 1.3 54.7 + - - +
97D HIS 4.5 0.2 - - - +
98D ARG* 2.7 43.0 + - + +
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Residues in contact with GLU 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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18D VAL* 5.4 0.5 - - - +
22D ILE* 3.0 32.2 - - - +
91D ILE* 2.8 30.5 + - + +
92D GLU* 3.1 14.8 + - + +
94D ALA* 1.3 75.1 - - - +
96D HIS* 1.3 66.8 + - - +
98D ARG* 3.2 30.1 + - - +
99D ASP* 4.4 9.4 - - - +
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Residues in contact with HIS 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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92D GLU 3.0 8.9 + - - +
93D TRP 3.7 1.3 - - - +
95D GLU* 1.3 81.4 - - - +
97D HIS* 1.3 84.3 + + + +
98D ARG 3.2 5.1 + - - -
99D ASP* 3.5 14.0 + - - +
100D SER* 3.6 12.8 + - - -
117D ASP* 3.0 25.1 - - - -
119D TRP* 3.0 44.9 - + + +
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Residues in contact with HIS 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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25D ARG* 5.5 0.4 - - - -
93D TRP* 2.9 60.4 + + + +
94D ALA* 5.1 0.2 - - - -
96D HIS* 1.3 89.5 + + + +
98D ARG* 1.3 59.6 + - - +
99D ASP 3.1 2.7 - - - -
100D SER* 2.7 29.8 + - - -
101D ASN 5.7 0.2 + - - -
102D PHE* 3.2 37.4 - - + -
117D ASP* 3.1 26.7 - - + -
119D TRP* 3.5 0.6 - + - -
120D ASP* 2.5 34.3 + - - -
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Residues in contact with ARG 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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21D LYS* 3.9 45.0 + - - +
22D ILE* 3.4 41.5 - - - +
24D GLU* 5.8 1.1 - - - +
25D ARG* 5.1 13.2 - - + +
94D ALA* 2.7 36.1 + - + +
95D GLU* 3.2 47.8 + - - +
96D HIS 3.2 0.4 + - - -
97D HIS* 1.3 79.0 - - - +
99D ASP* 1.3 68.9 + - - +
100D SER 3.2 3.2 + - - +
102D PHE* 5.1 1.6 - - - -
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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