Contacts of the helix formed by residues 79 - 89 (chain F) in PDB entry 4G7H
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 ASP 79 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F SER* 1.3 78.7 - - - +
80F PRO* 1.3 73.6 - - - +
81F VAL* 3.6 6.1 + - - +
82F ARG* 3.0 15.9 + - + +
83F GLN* 3.0 23.8 + - - +
8H G 2.5 48.4 + - - +
9H G 4.2 6.2 + - - +
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Residues in contact with PRO 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D ARG* 3.7 16.7 + - + +
573D MET* 6.1 0.2 - - + -
576D GLU* 3.9 30.7 - - + +
587D ARG* 5.0 2.7 - - - +
78F SER 3.6 8.0 - - - +
79F ASP* 1.3 92.1 - - - +
81F VAL* 1.3 56.5 + - + +
83F GLN* 3.6 13.4 - - + +
84F TYR* 2.9 30.0 + - - +
210F LEU* 3.6 25.0 - - + +
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Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ASP* 3.2 2.4 - - - +
80F PRO* 1.3 76.0 - - + +
82F ARG* 1.3 65.7 + - - +
84F TYR* 3.1 3.4 + - + +
85F LEU* 2.9 38.6 + - + +
209F PHE* 3.9 31.0 - - + -
210F LEU* 3.9 30.7 - - + -
8H G 3.4 48.7 - - + +
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Residues in contact with ARG 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ARG* 4.5 9.1 - - - +
243C ARG* 2.9 53.9 - - - +
244C PRO* 3.2 37.6 + - - +
245C GLY* 5.4 4.7 - - - -
246C ASP* 4.6 6.8 - - - +
79F ASP* 3.0 21.9 + - + +
81F VAL* 1.3 79.0 - - - +
83F GLN* 1.3 65.4 + - - +
85F LEU* 3.3 7.4 + - - +
86F HIS* 2.9 24.4 + - + +
7H G 4.4 8.1 + - - +
8H G 3.2 21.2 + - - +
9H G 3.9 1.4 + - - -
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Residues in contact with GLN 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D TYR* 3.4 15.7 + - - +
129D PHE 3.4 24.4 + - - -
130D SER* 3.5 19.7 + - - +
572D ARG* 3.5 28.8 + - - +
587D ARG* 5.8 1.7 + - - -
78F SER 5.2 7.5 + - - +
79F ASP 3.0 11.9 + - - +
80F PRO* 3.6 12.7 - - + +
82F ARG* 1.3 77.7 - - - +
84F TYR* 1.3 62.7 + - - +
86F HIS* 3.1 9.3 + - + +
87F GLU* 2.9 31.9 + - + +
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Residues in contact with TYR 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ILE* 4.0 11.2 - - + +
566D ILE* 4.9 0.9 - - - +
569D ASN* 3.3 46.9 - - + +
572D ARG* 4.3 3.6 - - - +
80F PRO 2.9 19.6 + - - +
81F VAL* 3.6 3.6 - - - +
83F GLN* 1.3 75.8 - - - +
85F LEU* 1.3 61.6 + - + +
87F GLU* 3.2 13.8 + - - +
88F ILE* 2.9 58.3 + - + +
192F LEU* 4.1 7.3 + - - +
196F VAL* 4.0 16.7 - - + +
210F LEU* 4.5 4.5 - - + -
213F ILE* 3.5 32.4 - - + +
214F GLN* 4.6 0.4 - - - -
217F ASN* 3.2 26.2 + - - -
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F VAL* 2.9 33.8 + - + +
82F ARG* 3.6 6.7 - - - +
84F TYR* 1.3 80.1 - - + +
86F HIS* 1.3 57.6 + - - +
88F ILE* 3.3 10.0 + - + +
89F GLY 3.0 23.2 + - - -
196F VAL* 3.9 31.9 - - + -
209F PHE* 5.6 1.8 - - + -
213F ILE* 5.7 0.9 - - + -
7H G 3.6 50.3 - - - +
8H G 3.5 39.3 - - + +
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Residues in contact with HIS 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C GLY* 4.4 17.3 + - - +
156D GLU* 4.9 8.9 + - - -
82F ARG* 2.9 15.4 + - + +
83F GLN* 3.1 12.3 + - + +
85F LEU* 1.3 78.1 - - - +
87F GLU* 1.3 70.6 + - + +
89F GLY* 3.3 6.4 + - - -
90F GLN* 3.2 45.9 + - + +
7H G 3.8 15.1 + - - +
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Residues in contact with GLU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D PHE 3.9 4.9 - - - +
155D ASP* 4.6 4.9 - - - +
565D ILE* 3.9 36.9 - - + +
568D ARG* 3.2 38.9 + - - +
569D ASN 5.1 0.3 + - - -
572D ARG* 2.8 31.6 + - - -
83F GLN* 2.9 23.4 + - + +
84F TYR* 3.6 13.1 - - - +
86F HIS* 1.3 79.3 - - + +
88F ILE* 1.3 67.1 + - - +
90F GLN* 3.3 22.4 + - - +
91F VAL 4.2 0.9 + - - -
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Residues in contact with ILE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ILE* 3.7 8.7 - - + -
84F TYR* 2.9 57.2 + - + +
85F LEU* 3.5 12.1 - - + +
86F HIS 3.3 0.2 - - - -
87F GLU* 1.3 76.6 - - - +
89F GLY* 1.3 62.6 + - - +
90F GLN 3.1 4.7 + - - -
91F VAL* 3.4 20.6 + - - +
189F GLU 5.3 1.6 - - - +
192F LEU* 3.5 42.8 - - + -
193F ARG* 3.7 30.4 + - + +
196F VAL* 4.8 2.2 - - + -
7H G 4.3 14.8 - - + +
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Residues in contact with GLY 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F LEU 3.0 10.1 + - - -
86F HIS 3.3 1.5 + - - -
87F GLU 3.2 1.0 - - - -
88F ILE* 1.3 75.9 - - - +
90F GLN* 1.3 67.6 + - - +
91F VAL 3.3 1.0 - - - -
92F PRO 5.1 0.2 - - - -
193F ARG* 3.6 15.0 + - - -
7H G 3.3 38.8 - - - +
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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