Contacts of the helix formed by residues 115 - 124 (chain B) in PDB entry 1RYF
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 LYS 115 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 4.5 7.6 + - - +
111B ASN* 2.9 26.8 + - + +
113B ARG 3.4 0.4 - - - -
114B ALA* 1.3 80.3 - - - +
116B TRP* 1.3 102.2 + - + +
117B TYR 3.5 1.6 - - - -
118B PRO* 3.5 4.3 - - - +
119B GLU* 3.0 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.8 28.0 - - + -
10B GLY* 3.5 37.0 - - - -
11B ASP* 2.9 31.4 + - - +
58B THR* 5.8 2.0 - - - -
99B ILE* 3.8 25.6 - - + -
100B CYS 5.1 1.8 - - - -
108B SER 5.1 1.8 - - - -
111B ASN* 2.9 35.4 + - + +
112B VAL* 4.1 4.5 - - - +
115B LYS* 1.3 104.2 - - + +
117B TYR* 1.3 67.3 + - - +
119B GLU* 3.3 28.4 + - + +
120B VAL* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 3.8 12.7 - - + +
112B VAL 2.9 19.7 + - - +
113B ARG* 4.0 9.6 - - + -
116B TRP* 1.3 76.6 - - - +
118B PRO* 1.3 77.3 - - + +
120B VAL* 3.9 2.2 - - - +
121B ARG* 3.0 51.7 + - + +
129B ILE* 4.4 6.1 - - + -
167B GLU 4.6 7.0 + - - -
168B ILE* 3.3 55.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG 3.2 28.5 - - - +
114B ALA 3.8 12.3 - - - +
115B LYS 3.5 12.8 - - - +
117B TYR* 1.3 100.6 - - + +
119B GLU* 1.3 55.9 + - - +
121B ARG* 3.3 5.7 + - + +
122B HIS* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LYS* 3.0 34.8 + - - +
116B TRP* 3.3 34.1 + - + +
118B PRO* 1.3 77.1 - - - +
120B VAL* 1.3 63.0 + - + +
122B HIS* 3.4 9.3 + - + +
123B HIS* 3.3 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.4 14.6 - - + -
97B PHE* 3.6 52.5 - - + -
99B ILE* 4.3 11.4 - - + -
116B TRP* 2.9 19.8 + - + +
117B TYR 3.9 3.4 - - - +
119B GLU* 1.3 76.6 - - + +
121B ARG* 1.3 67.3 + - - +
123B HIS* 3.3 5.1 + - - +
124B CYS* 2.9 27.1 + - - +
129B ILE* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 3.0 46.5 + - + +
118B PRO* 4.0 4.3 - - + +
120B VAL* 1.3 81.2 - - - +
122B HIS* 1.3 66.6 + - - +
123B HIS 3.4 0.2 + - - -
124B CYS 2.8 33.9 + - - -
125B PRO* 3.4 42.2 + - - +
126B ASN 4.6 2.6 + - - -
127B THR* 2.9 33.3 + - - +
128B PRO* 4.6 1.2 - - - +
129B ILE* 3.4 30.7 - - + +
168B ILE 4.9 2.0 + - - -
169B GLY 4.7 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO 2.9 17.6 + - - +
119B GLU* 3.6 9.9 - - + +
120B VAL 3.3 0.2 - - - -
121B ARG* 1.3 78.4 - - - +
123B HIS* 1.3 83.7 + + - +
125B PRO* 5.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 5.9 0.9 - - + -
119B GLU* 3.3 31.2 - - + +
120B VAL* 3.3 5.6 + - - +
122B HIS* 1.3 103.8 - + - +
124B CYS* 1.3 75.3 + - - +
125B PRO* 3.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 5.2 13.0 - - + -
94B ALA* 5.6 2.9 - - - -
97B PHE* 3.8 29.6 - - + -
120B VAL 2.9 13.5 + - - +
121B ARG* 2.8 27.7 + - - -
122B HIS 3.5 0.6 - - - -
123B HIS* 1.3 94.7 - - - +
125B PRO* 1.3 61.4 - - - +
126B ASN 3.3 2.4 + - - -
127B THR* 3.2 26.2 - - + -
----------------------------------------------------------
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