Contacts of the helix formed by residues 77 - 88 (chain G) in PDB entry 1H4O
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 77 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PRO* 5.8 2.0 - - + -
76G ASN* 1.3 78.4 + - - +
78G ALA* 1.3 63.3 + - - +
79G PHE* 3.0 21.1 + - + +
80G VAL* 3.0 43.4 + - - +
81G THR* 3.1 18.0 + - - +
98G ALA* 3.8 0.2 - - - -
100G PRO* 4.2 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G PHE* 4.0 13.2 - - + -
17G GLY 3.2 15.7 - - - +
18G GLU* 3.5 33.0 - - - +
19G PRO* 3.6 8.9 - - + +
77G ASP* 1.3 71.1 - - - +
79G PHE* 1.3 65.4 + - - +
81G THR* 3.3 11.5 + - - +
82G GLY 3.0 17.8 + - - -
98G ALA* 3.6 14.5 - - + +
100G PRO* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLY 4.4 3.7 - - - +
18G GLU* 4.4 11.4 - - + -
19G PRO* 3.4 37.9 - - + -
77G ASP* 3.0 15.3 + - + +
78G ALA* 1.3 77.5 - - - +
80G VAL* 1.3 63.7 + - + +
82G GLY* 4.0 0.3 - - - -
83G GLU* 3.2 30.1 + - + +
86G ARG* 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ALA* 3.7 24.7 - - + +
43G PHE* 3.6 19.5 - - + -
76G ASN* 4.0 15.0 - - + +
77G ASP* 3.0 30.5 + - - +
79G PHE* 1.3 75.4 - - + +
81G THR* 1.3 66.0 + - - +
83G GLU* 3.3 3.1 + - - -
84G TRP* 2.9 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G PHE 5.0 0.2 + - - -
17G GLY 4.7 2.4 + - - -
42G ALA* 4.7 3.8 - - + -
74G SER* 3.6 24.2 - - - +
76G ASN* 3.7 11.4 - - + +
77G ASP 3.1 12.1 + - - +
78G ALA* 3.3 17.3 + - - +
79G PHE 3.5 0.2 - - - -
80G VAL* 1.3 75.6 - - - +
82G GLY* 1.3 60.6 + - - +
84G TRP* 3.3 8.6 + - + +
85G GLY 2.9 25.3 + - - -
96G LEU* 3.8 29.2 + - + +
97G LEU 4.5 2.5 - - - +
98G ALA* 3.5 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLY* 4.1 11.2 - - - -
78G ALA 3.0 17.4 + - - -
79G PHE 4.0 0.2 - - - -
81G THR* 1.3 78.3 + - - +
83G GLU* 1.3 62.1 + - - +
85G GLY* 3.4 1.3 + - - -
86G ARG* 3.1 49.9 + - - +
96G LEU* 5.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PHE* 4.0 12.3 - - + -
79G PHE* 3.2 19.5 + - + +
80G VAL* 3.8 4.3 - - - +
82G GLY* 1.3 75.7 - - - +
84G TRP* 1.3 64.2 + - - +
86G ARG* 2.7 40.3 + - - +
87G ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 84 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 4.0 23.6 - - + -
42G ALA* 3.6 20.4 - - + -
43G PHE* 3.1 46.0 - + + +
47G CYS* 3.7 28.3 - - + -
48G SER* 2.9 24.5 + - - -
52G LEU* 3.7 24.7 - - + -
72G CYS* 4.0 10.3 - - - -
74G SER* 5.1 3.6 - - - -
80G VAL 2.9 19.1 + - - +
81G THR* 3.6 6.1 - - - +
82G GLY 3.3 0.2 - - - -
83G GLU* 1.3 77.4 - - - +
85G GLY* 1.3 60.9 + - - +
87G ALA* 3.2 9.4 + - - +
88G HIS* 3.2 36.0 - + - -
96G LEU* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 4.9 3.8 - - - -
81G THR 2.9 12.6 + - - -
82G GLY* 3.4 2.0 + - - -
84G TRP* 1.3 75.0 - - - +
86G ARG* 1.3 63.1 + - - +
88G HIS 3.0 11.6 + - - -
89G LYS 3.0 10.0 + - - -
90G ALA* 3.1 14.4 + - - -
91G GLU 5.5 0.7 - - - -
96G LEU* 3.7 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLY* 3.8 32.3 + - - -
79G PHE 5.0 0.6 + - - -
82G GLY* 3.1 28.7 + - - +
83G GLU* 2.7 45.4 + - - +
85G GLY* 1.3 76.8 - - - +
87G ALA* 1.3 61.4 + - - +
88G HIS 3.1 1.2 + - - -
89G LYS* 3.3 15.4 + - - +
90G ALA 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PHE* 4.7 10.8 - - + -
83G GLU 3.0 13.7 + - - +
84G TRP* 3.2 13.2 + - - +
86G ARG* 1.3 75.3 - - - +
88G HIS* 1.3 74.5 + - + +
89G LYS* 3.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PHE* 5.8 0.8 - - - -
48G SER* 3.2 29.9 + - - -
49G LYS* 3.5 20.5 + - + -
52G LEU* 3.9 25.4 - - + -
53G PRO* 4.5 9.7 - - + +
56G VAL* 4.0 16.1 - - + +
84G TRP* 3.2 50.6 + + - +
85G GLY 3.0 4.4 + - - +
87G ALA* 1.3 87.1 + - + +
89G LYS* 1.3 74.5 + - - +
90G ALA* 3.2 3.5 + - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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