Contacts of the helix formed by residues 121 - 128 (chain H) in PDB entry 7C17
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 PRO 121 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ARG* 5.2 1.8 - - - -
119H ASP 3.8 5.8 - - - +
120H CYS* 1.3 84.9 - - + +
122H ILE* 1.3 67.6 + - + +
123H ILE 3.3 2.5 - - - -
124H GLU* 3.2 15.7 + - + +
125H ASN* 2.8 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G SER* 5.0 4.3 - - - +
108H LEU* 3.4 25.1 - - - +
109H ALA* 3.8 18.4 - - - +
110H ASN 3.7 14.1 - - - +
111H ALA* 3.7 24.2 - - + -
120H CYS* 3.2 15.0 - - + -
121H PRO* 1.3 84.5 - - + +
123H ILE* 1.3 63.6 + - + +
125H ASN* 3.3 15.9 + - + +
126H LEU* 2.9 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU* 5.3 4.2 - - + +
66G LEU* 4.7 21.8 - - + +
69G LEU* 4.1 24.2 - - + -
70G PHE* 3.6 34.3 - - + -
75G ARG* 4.3 15.5 - - + +
77G SER* 4.6 21.1 - - - +
80G VAL* 5.5 2.5 - - + -
120H CYS 3.9 16.2 - - - +
121H PRO 3.3 0.4 - - - -
122H ILE* 1.3 77.0 - - + +
124H GLU* 1.3 59.1 + - - +
126H LEU* 3.2 14.1 + - + +
127H SER* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G GLN* 5.8 1.7 + - - -
45G ASN* 2.8 27.0 + - - -
70G PHE* 3.2 26.6 - - + -
75G ARG* 5.0 7.0 + - - +
120H CYS 5.1 0.2 + - - -
121H PRO* 3.2 21.2 + - + +
123H ILE* 1.3 79.1 - - - +
125H ASN* 1.3 62.5 + - - +
127H SER* 2.7 33.5 + - - -
128H GLY* 3.3 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H LEU* 3.9 23.6 - - + +
121H PRO* 2.8 30.2 + - - +
122H ILE* 3.6 20.7 - - + +
123H ILE 3.3 0.2 - - - -
124H GLU* 1.3 79.9 - - - +
126H LEU* 1.3 60.6 + - - +
127H SER 3.5 0.2 + - - -
128H GLY* 3.9 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU* 5.0 1.9 - - - +
52G GLN* 3.8 23.6 - - + +
58G PHE* 5.7 11.9 - - + -
66G LEU* 5.9 9.6 - - + -
104H GLN* 5.0 6.7 - - + +
105H LEU* 5.9 3.4 - - + -
108H LEU* 3.4 46.4 - - + +
109H ALA* 5.0 8.7 - - + -
122H ILE* 2.9 16.3 + - + +
123H ILE* 3.2 13.9 + - + +
125H ASN* 1.3 74.5 - - - +
127H SER* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ASN* 3.1 20.7 + - - -
48G THR* 4.2 16.7 + - - +
49G LEU* 3.7 26.4 - - - +
52G GLN* 4.5 8.5 + - - +
70G PHE* 4.2 4.3 - - - -
123H ILE 2.9 13.0 + - - -
124H GLU* 2.7 31.2 + - - -
125H ASN 3.2 0.2 - - - -
126H LEU* 1.3 80.3 - - - +
128H GLY* 1.3 77.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ASN* 5.3 2.2 - - - -
48G THR* 4.4 14.6 + - - +
124H GLU* 3.3 7.0 + - - -
125H ASN* 3.9 7.7 + - - -
126H LEU 3.6 1.2 - - - -
127H SER* 1.3 91.3 + - - +
----------------------------------------------------------
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