Contacts of the helix formed by residues 66 - 85 (chain D) in PDB entry 6N1G
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 SER 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B TYR* 4.2 0.8 + - - -
64D TYR 4.2 1.4 + - - -
65D GLY* 1.3 75.8 - - - +
67D TYR* 1.3 72.5 + - - +
68D LEU* 3.9 11.6 + - - +
69D GLY* 3.2 16.0 + - - +
70D VAL* 3.4 14.7 + - - +
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Residues in contact with TYR 67 (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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66D SER* 1.3 81.1 - - - +
68D LEU* 1.3 55.7 + - - +
70D VAL* 3.3 10.2 - - + +
71D ASN* 2.4 40.2 + - - +
214D GLY 5.0 6.1 - - - +
215D VAL* 4.4 13.2 - - + +
218D GLY 5.4 1.1 - - - -
219D MET* 3.1 63.3 - - + +
402D GOL 5.8 3.1 - - - -
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 5.8 2.5 - - + -
66D SER* 3.2 7.7 + - - +
67D TYR* 1.3 79.3 - - - +
69D GLY* 1.3 58.0 + - - +
71D ASN* 3.9 0.9 - - - -
72D LEU* 2.8 41.7 + - + +
211D VAL* 4.0 23.6 - - + -
215D VAL* 3.8 25.2 - - + +
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Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.9 17.8 + - - -
68B LEU* 3.6 28.9 - - - +
215B VAL* 4.5 9.4 - - - +
54D SER* 5.2 2.1 + - - -
66D SER* 3.2 14.7 + - - -
68D LEU* 1.3 79.8 - - - +
70D VAL* 1.3 58.2 + - - +
72D LEU* 4.2 0.9 - - - -
73D GLY* 3.6 14.4 + - - -
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 4.1 10.1 - - - +
54D SER* 4.8 16.6 - - - +
55D VAL* 5.2 12.8 - - + -
58D MET* 5.3 6.3 - - + -
63D LYS* 4.6 10.5 - - - +
65D GLY 4.9 4.3 - - - +
66D SER 3.4 12.8 + - - +
67D TYR* 3.3 17.3 - - - +
69D GLY* 1.3 78.3 - - - +
71D ASN* 1.3 72.8 + - - +
73D GLY 4.0 0.9 - - - -
74D PHE* 3.1 29.1 + - - +
223D TYR* 3.5 10.5 + - + +
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Residues in contact with ASN 71 (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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67D TYR* 2.4 25.8 + - - +
68D LEU* 3.9 4.3 - - - +
70D VAL* 1.3 79.2 - - - +
72D LEU* 1.3 56.4 + - - +
74D PHE* 3.2 1.6 + - - +
75D GLY 2.7 32.1 + - - -
210D VAL* 4.6 1.5 - - - +
211D VAL* 3.2 30.9 + - + +
214D GLY* 2.8 38.5 + - - +
215D VAL* 2.9 11.6 + - - +
223D TYR* 3.1 31.2 + - - -
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Residues in contact with LEU 72 (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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68B LEU* 4.3 25.1 - - + -
72B LEU* 5.0 12.8 - - + -
68D LEU* 2.8 31.8 + - + +
69D GLY* 4.7 3.6 - - - -
71D ASN* 1.3 73.4 - - - +
73D GLY* 1.3 56.4 + - - +
76D PHE* 2.8 79.1 + - + -
208D ILE* 5.2 4.9 - - + -
211D VAL* 3.5 22.6 - - + +
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Residues in contact with GLY 73 (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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68B LEU* 5.9 2.8 - - - +
211B VAL* 6.5 1.1 - - - -
212B ILE* 3.9 15.1 - - - +
215B VAL* 4.7 17.3 - - - -
50D PHE* 4.6 7.5 - - - +
54D SER* 5.0 3.1 - - - -
69D GLY 3.6 15.1 + - - -
70D VAL 4.3 0.2 - - - -
71D ASN 3.2 0.6 - - - -
72D LEU* 1.3 78.6 - - - +
74D PHE* 1.3 58.6 + - - +
76D PHE* 4.0 5.3 - - - +
77D GLY* 3.0 21.7 + - - -
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Residues in contact with PHE 74 (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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47D MET* 4.1 30.6 - - + +
48D MET* 5.7 2.0 - - + -
51D GLY* 3.7 26.4 - - - +
54D SER* 5.4 0.8 + - - -
70D VAL 3.1 20.9 + - - +
71D ASN* 3.8 2.2 - - - +
73D GLY* 1.3 75.9 - - - +
75D GLY* 1.3 61.2 + - - +
77D GLY* 3.0 2.5 + - - -
78D VAL* 2.9 54.1 + - + +
210D VAL* 4.2 16.6 - - + -
223D TYR* 3.5 35.9 - + - +
225D ILE* 5.9 3.4 - - + -
229D ARG* 4.0 38.1 - - + -
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Residues in contact with GLY 75 (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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71D ASN 2.7 19.5 + - - -
74D PHE* 1.3 70.7 - - - +
76D PHE* 1.3 62.9 + - - +
78D VAL* 3.5 1.6 + - - +
79D THR* 3.2 12.0 + - - -
207D GLY* 2.9 31.2 - - - -
210D VAL* 3.1 29.8 - - - +
211D VAL* 3.8 1.3 - - - -
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Residues in contact with PHE 76 (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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68B LEU* 6.4 0.2 - - + -
72B LEU* 4.6 15.9 - - + -
76B PHE* 6.2 0.4 - + - -
208B ILE* 3.9 39.9 - - + -
211B VAL* 4.8 9.9 - - + -
212B ILE* 3.5 23.1 - - + +
72D LEU* 2.8 62.4 + - + +
73D GLY* 4.0 2.2 - - - +
74D PHE 3.3 0.2 - - - -
75D GLY* 1.3 78.6 - - - +
77D GLY* 1.3 62.3 + - - +
79D THR* 3.2 8.8 + - - -
80D MET* 3.1 25.6 + - - +
204D LEU* 4.8 8.7 - - + -
207D GLY* 5.4 0.2 - - - -
208D ILE* 4.4 20.6 - - + -
211D VAL* 4.7 1.8 - - + -
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Residues in contact with GLY 77 (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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212B ILE* 3.8 2.9 - - - +
46D VAL* 4.0 7.1 - - - +
47D MET* 4.6 8.6 - - - +
50D PHE* 4.0 26.2 - - - -
73D GLY 3.0 17.6 + - - -
74D PHE* 3.0 4.8 + - - -
76D PHE* 1.3 74.4 - - - +
78D VAL* 1.3 58.9 + - - +
80D MET* 3.2 5.8 + - - +
81D GLY* 3.0 22.7 + - - -
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Residues in contact with VAL 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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47D MET* 3.9 33.2 - - + -
74D PHE* 2.9 43.5 + - + +
75D GLY* 3.9 7.9 - - - +
76D PHE 3.4 0.2 - - - -
77D GLY* 1.3 75.3 - - - +
79D THR* 1.3 57.9 + - - +
81D GLY* 3.4 1.9 + - - -
82D VAL* 3.1 26.0 + - - +
93D MET* 5.8 1.7 - - + +
206D ILE* 4.8 10.5 - - + -
207D GLY* 5.3 2.0 - - - -
210D VAL* 4.6 7.4 - - + -
403D GOL 4.5 18.6 - - - +
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Residues in contact with THR 79 (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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205B VAL* 5.3 2.0 - - + -
75D GLY 3.2 14.7 + - - -
76D PHE* 3.2 11.9 + - - -
77D GLY 3.1 1.0 - - - -
78D VAL* 1.3 75.3 - - - +
80D MET* 1.3 77.1 + - + +
82D VAL* 3.2 6.2 + - - +
83D HIS* 3.0 27.6 + - + +
203D ALA* 2.4 46.8 + - + +
204D LEU* 3.6 19.8 + - + +
206D ILE* 6.1 0.2 - - - -
207D GLY* 3.2 11.5 - - - +
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Residues in contact with MET 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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185B CYS* 4.2 22.4 - - - -
189B ILE* 5.1 0.7 - - - -
205B VAL* 3.1 36.1 - - + +
208B ILE* 3.6 17.5 - - + -
209B LEU* 4.2 19.7 - - + -
212B ILE* 3.7 15.3 - - + -
46D VAL* 4.2 13.7 - - + -
50D PHE* 4.4 7.2 - - + -
76D PHE 3.1 15.9 + - - +
77D GLY 3.2 6.3 + - - +
79D THR* 1.3 93.7 - - + +
81D GLY* 1.3 57.7 + - - +
83D HIS* 3.7 5.7 - - + +
84D VAL* 2.8 34.8 + - - +
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Residues in contact with GLY 81 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D SER* 2.6 38.8 + - - -
46D VAL* 4.4 3.7 - - - +
47D MET* 5.4 1.3 - - - -
77D GLY 3.0 13.3 + - - -
78D VAL* 3.4 6.2 + - - -
79D THR 3.2 0.2 - - - -
80D MET* 1.3 74.3 - - - +
82D VAL* 1.3 65.1 + - - +
84D VAL* 3.2 13.0 - - - +
85D ALA* 3.5 5.7 + - - +
91D ALA* 4.4 2.9 - - - +
93D MET* 5.0 4.7 - - - -
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Residues in contact with VAL 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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195B ASN* 4.5 15.8 + - - +
78D VAL 3.1 14.5 + - - +
79D THR* 3.2 8.7 + - - +
81D GLY* 1.3 73.9 - - - +
83D HIS* 1.3 65.4 + - - +
86D GLY* 3.0 25.5 + - - -
91D ALA* 3.7 14.4 - - + -
93D MET* 6.4 0.2 - - + -
202D GLU* 6.1 1.1 - - + -
203D ALA* 3.3 29.8 - - + -
206D ILE* 4.7 5.6 - - + -
403D GOL 3.0 41.7 - - - +
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Residues in contact with HIS 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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185B CYS* 5.7 3.1 - - - -
188B ALA* 2.9 34.5 + - + -
189B ILE* 2.9 38.6 + - + +
194B ASN* 3.7 12.2 + - - -
195B ASN* 4.9 10.1 - - + +
196B PRO 6.0 0.7 - - - -
198B LEU* 3.4 32.7 - - + +
205B VAL* 4.7 7.3 - - + +
79D THR* 3.0 17.9 + - + +
80D MET* 3.7 11.4 - - + +
82D VAL* 1.3 80.8 - - - +
84D VAL* 1.3 64.8 + - - +
86D GLY 3.9 2.9 + - - -
203D ALA* 4.4 7.5 - - + +
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Residues in contact with VAL 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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184B LEU* 3.4 32.5 - - + -
185B CYS* 5.2 5.4 - - - -
188B ALA* 4.1 16.8 - - + +
194B ASN* 3.3 15.6 + - - -
276B ILE* 3.3 32.9 - - + +
42D MET* 4.3 6.1 - - + -
43D SER* 3.9 16.8 - - - +
46D VAL* 4.9 9.4 - - + -
80D MET 2.8 24.2 + - - +
81D GLY* 3.2 17.9 - - - +
83D HIS* 1.3 75.9 - - - +
85D ALA* 1.3 66.3 + - + +
88D ILE* 4.2 1.7 - - - +
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Residues in contact with ALA 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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276B ILE* 4.5 3.1 - - + -
39D ALA* 3.6 26.9 - - + +
42D MET* 4.9 0.7 - - + -
43D SER* 3.6 29.6 - - - +
81D GLY 3.5 3.3 + - - -
82D VAL 3.6 2.7 - - - -
83D HIS 3.4 0.2 - - - -
84D VAL* 1.3 82.1 - - + +
86D GLY* 1.3 59.2 + - - +
87D ARG 3.7 0.7 - - - -
88D ILE* 4.0 9.6 - - - -
89D SER* 2.6 31.3 + - - +
91D ALA* 3.4 5.3 + - - -
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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