Contacts of the helix formed by residues 78 - 88 (chain X) in PDB entry 3F6E
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 ALA 78 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47X GLU* 3.7 12.3 - - + +
48X ALA* 4.3 3.4 - - - +
51X VAL* 3.5 29.2 - - + -
69X LEU* 3.8 15.5 - - + -
74X GLY 3.4 2.2 + - - +
75X THR 3.0 11.8 + - - +
77X ASN* 1.3 77.9 - - - +
79X MET* 1.4 57.1 + - - +
80X GLY 3.4 2.9 - - - -
81X ALA* 3.1 8.0 + - - +
82X LEU* 3.0 30.6 + - + +
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Residues in contact with MET 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X THR* 3.5 15.5 - - + +
76X GLY* 3.0 25.0 + - - +
77X ASN 3.4 0.4 - - - -
78X ALA* 1.4 75.2 - - - +
80X GLY* 1.3 66.2 + - - +
82X LEU* 3.2 14.3 + - + +
83X SER* 3.0 17.8 + - - -
118X LEU* 3.1 42.2 - - + +
119X PRO* 3.8 18.6 - - + +
120X ARG 4.6 4.9 - - - +
121X PRO* 6.0 0.7 - - + -
122X LEU* 3.3 21.9 - - + +
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Residues in contact with GLY 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76X GLY 4.9 0.4 + - - -
77X ASN 4.9 2.0 + - - -
78X ALA 3.4 0.6 - - - -
79X MET* 1.3 76.9 - - - +
81X ALA* 1.3 61.6 + - - +
83X SER* 2.7 27.6 + - - -
84X ASN* 3.5 10.4 + - - -
402X GLY* 5.3 2.3 - - - -
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Residues in contact with ALA 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X ALA* 4.0 24.1 - - + +
51X VAL* 3.7 28.3 - - + +
52X GLY* 4.4 5.6 - - - +
55X ASP* 4.4 3.5 - - - +
78X ALA* 3.1 12.1 + - - +
80X GLY* 1.3 75.7 - - - +
82X LEU* 1.3 63.1 + - - +
84X ASN* 3.2 13.0 + - - +
85X ALA* 3.1 20.6 + - - +
404X GLY 6.2 0.2 - - - +
405X PHE* 6.0 0.4 - - - -
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Residues in contact with LEU 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X VAL* 4.0 17.7 - - + -
69X LEU* 6.2 0.2 - - + -
75X THR* 5.2 5.4 - - + +
78X ALA* 3.0 22.8 + - + +
79X MET* 3.6 18.8 - - + +
80X GLY 3.2 0.8 - - - -
81X ALA* 1.3 73.6 - - - +
83X SER* 1.3 59.9 - - - +
85X ALA* 3.7 2.0 - - - +
86X TRP* 2.9 31.9 + - - +
92X LEU* 4.6 4.7 - - + -
94X VAL* 3.9 34.1 - - + -
119X PRO* 4.4 23.3 - - + +
122X LEU* 4.1 20.0 - - + +
123X VAL* 4.5 8.3 - - + -
153X PRO* 4.1 18.4 - - + -
155X TYR* 5.7 0.4 - - + -
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Residues in contact with SER 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X MET 3.0 11.4 + - - -
80X GLY* 2.7 21.8 + - - -
82X LEU* 1.3 79.4 - - - +
84X ASN* 1.3 64.1 + - - +
86X TRP* 3.5 4.2 + - - +
87X ASN* 3.4 12.5 + - - +
122X LEU* 3.7 24.6 - - - +
400X ALA* 3.4 23.7 - - - +
402X GLY* 5.0 5.5 - - - -
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Residues in contact with ASN 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X ASP* 4.6 2.0 - - - +
80X GLY 3.5 9.6 + - - -
81X ALA* 3.2 12.6 + - - +
83X SER* 1.3 83.8 + - - +
85X ALA* 1.4 61.9 + - - +
87X ASN 3.0 2.9 + - - -
88X SER* 3.0 23.9 + - - -
398X CYS* 3.5 7.4 - - - -
399X ALA* 3.4 12.7 + - - +
400X ALA* 2.9 31.0 + - - +
402X GLY* 2.9 44.1 + - - -
403X LEU 5.2 0.4 + - - -
405X PHE* 3.7 27.6 - - + +
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Residues in contact with ALA 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X VAL* 5.3 0.2 - - + -
55X ASP* 3.7 11.6 + - - +
81X ALA 3.1 11.3 + - - +
82X LEU* 3.1 10.1 + - - +
84X ASN* 1.4 76.2 - - - +
86X TRP* 1.3 63.5 + - - +
88X SER* 3.5 8.3 - - - -
89X HIS 3.2 2.9 + - - -
90X SER* 3.0 29.6 + - - -
92X LEU* 3.6 30.7 - - + -
153X PRO* 3.7 15.2 - - + +
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Residues in contact with TRP 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X LEU 2.9 16.1 + - - +
83X SER* 3.7 7.2 - - - +
85X ALA* 1.3 77.9 - - - +
87X ASN* 1.3 76.3 + - - +
89X HIS* 3.2 22.6 + + - -
121X PRO 4.3 12.1 + - - -
122X LEU* 3.4 36.1 - - + +
123X VAL* 3.5 29.6 - - - -
124X LYS* 3.7 18.4 - - + -
152X GLY* 5.6 1.1 - - - -
153X PRO* 3.8 12.0 - - + +
301X ASP* 5.9 1.6 - - - -
303X LEU* 4.0 27.7 - - + +
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Residues in contact with ASN 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X SER 3.4 3.9 + - - +
84X ASN 3.0 4.7 + - - +
86X TRP* 1.3 96.4 - - - +
88X SER* 1.3 58.9 + - - +
89X HIS* 3.3 8.6 + - - -
209X PRO* 5.2 4.9 - - - +
238X PRO* 4.9 4.2 - - - +
279X ARG* 3.5 47.7 + - - +
304X GLU* 5.6 0.2 - - - +
399X ALA* 2.9 38.8 + - + +
400X ALA* 3.5 16.9 - - - +
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Residues in contact with SER 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X ASP* 4.4 0.3 + - - -
59X GLN* 3.7 25.0 + - - +
84X ASN 3.0 13.2 + - - -
85X ALA* 3.3 4.9 + - - -
86X TRP 3.3 0.2 - - - -
87X ASN* 1.3 76.2 - - - +
89X HIS* 1.3 72.5 + - - +
90X SER* 2.6 26.6 + - - -
209X PRO* 5.7 6.4 - - - +
210X ASP* 4.5 3.9 - - - +
213X ALA* 5.6 3.5 - - - +
238X PRO* 4.9 9.0 - - - -
239X ARG* 5.3 7.4 + - - -
399X ALA* 3.6 16.8 - - - -
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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