Contacts of the helix formed by residues 95 - 104 (chain H) in PDB entry 5GAG
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 GLY 95 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H SER 3.8 2.6 + - - -
94H ILE* 1.3 77.8 - - - +
96H THR* 1.3 65.8 + - - -
97H ARG* 3.3 4.3 - - - -
98H ASP* 3.4 16.0 + - - -
99H ILE* 3.3 21.3 + - - +
117H LEU* 4.6 2.7 - - - -
121H VAL* 4.1 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2221A G 4.9 1.6 + - - -
95H GLY* 1.3 71.2 - - - -
97H ARG* 1.3 62.1 + - - +
98H ASP 3.2 0.4 - - - -
99H ILE* 4.7 0.7 - - - +
100H ALA* 2.9 32.9 + - - +
112H LYS* 3.4 36.4 + - - +
115H VAL* 3.7 38.1 - - + +
117H LEU* 3.9 21.5 - - + +
121H VAL* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2219A U 4.3 6.5 + - - -
2220A U 3.5 39.9 + - - -
95H GLY* 3.3 2.4 - - - -
96H THR* 1.3 82.2 + - - +
98H ASP* 1.3 60.5 + - - +
100H ALA* 4.5 0.9 - - - -
101H ASP* 2.9 58.3 + - - +
112H LYS* 3.5 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H ILE* 3.8 11.5 - - + +
93H SER 4.0 9.7 - - - +
94H ILE* 3.6 25.9 - - + +
95H GLY* 3.4 18.3 + - - +
96H THR 3.2 0.6 - - - -
97H ARG* 1.3 81.1 - - - +
99H ILE* 1.3 59.6 + - - +
101H ASP* 3.8 2.5 - - - +
102H ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H VAL* 4.8 2.2 - - + -
80H ILE* 4.4 2.9 - - + -
94H ILE* 3.9 13.2 - - + -
95H GLY 3.3 18.1 + - - +
96H THR 4.2 1.8 - - - +
98H ASP* 1.3 73.3 - - - +
100H ALA* 1.3 60.8 + - - +
102H ALA* 4.3 3.8 - - - -
103H VAL* 2.9 41.5 + - + +
115H VAL* 4.3 7.4 - - + -
117H LEU* 3.5 34.1 - - + -
122H LEU* 4.0 12.3 - - + -
130H VAL* 3.6 15.9 - - + -
132H PHE* 4.1 21.1 - - + -
144H VAL* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H THR 2.9 19.5 + - - +
97H ARG 4.2 0.9 - - - +
99H ILE* 1.3 76.4 - - - +
101H ASP* 1.3 65.0 + - - +
103H VAL* 3.8 4.0 - - - +
104H THR* 2.9 33.6 + - - +
110H VAL* 3.5 9.3 - - - +
111H ALA 3.6 24.2 - - - +
112H LYS* 3.6 13.9 - - + +
115H VAL* 3.7 8.2 - - + +
132H PHE* 5.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ARG* 2.9 43.4 + - - +
98H ASP* 3.8 2.7 - - - +
100H ALA* 1.3 82.8 - - - +
102H ALA* 1.3 60.5 + - - +
103H VAL 3.5 0.2 - - - -
104H THR* 3.1 18.6 + - - +
105H ALA* 3.7 14.9 + - - +
112H LYS* 5.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H VAL* 3.6 16.2 - - + +
79H THR 4.8 6.1 - - - +
80H ILE* 3.6 23.1 - - + -
98H ASP 2.9 20.5 + - - +
99H ILE 3.9 1.1 - - - +
101H ASP* 1.3 79.8 - - - +
103H VAL* 1.3 58.1 + - - +
104H THR 3.5 0.4 - - - -
105H ALA* 3.7 5.1 + - - +
106H ALA* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ILE* 5.6 3.1 - - + -
76H GLU* 5.2 2.7 - - - +
78H VAL* 3.7 31.0 - - + -
99H ILE* 2.9 28.9 + - + +
100H ALA* 4.2 3.6 - - - +
102H ALA* 1.3 75.3 - - - +
104H THR* 1.3 60.9 + - - +
105H ALA 3.2 1.6 - - - -
106H ALA* 3.3 13.6 + - + -
107H GLY 3.4 0.5 + - - -
108H VAL* 2.8 38.0 + - + +
110H VAL* 3.6 28.7 - - + -
132H PHE* 4.3 11.9 - - + -
142H VAL* 5.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H ALA 2.9 28.9 + - - +
101H ASP* 3.1 21.9 + - - +
103H VAL* 1.3 74.7 - - - +
105H ALA* 1.3 57.5 + - - +
107H GLY* 4.3 5.1 + - - -
108H VAL 3.0 15.6 + - - +
109H GLU* 3.7 26.1 - - - +
110H VAL 3.3 18.8 - - - +
----------------------------------------------------------
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