Contacts of the strand formed by residues 118 - 122 (chain Y) in PDB entry 1I9R
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 SER 118 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137X SER* 4.7 11.0 - - - -
116Y ALA 3.9 1.2 + - - -
117Y PRO* 1.3 72.9 - - - +
119Y VAL* 1.3 59.4 + - - +
120Y PHE* 2.8 36.5 - - - -
141Y ASN* 2.8 40.1 + - - +
142Y ASN* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137X SER* 3.6 8.9 + - - -
117Y PRO* 3.7 9.8 + - + +
118Y SER* 1.3 70.9 - - - +
120Y PHE* 1.3 70.0 + - - +
138Y CYS* 5.1 3.8 - - - -
139Y LEU 3.0 9.0 - - - +
140Y LEU* 4.1 12.8 - - + -
198Y CYS* 5.1 2.0 - - - -
200Y VAL* 3.2 36.1 - - + -
205Y LEU* 5.3 0.4 - - + -
209Y VAL* 4.0 20.4 - - + +
211Y LYS* 3.4 48.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134X LYS 4.0 4.9 - - - -
135X SER* 3.4 26.0 - - - -
137X SER* 3.7 27.1 - - - -
140X THR* 4.5 12.3 - - - -
142X ALA* 3.3 34.3 - - + -
188X THR* 4.8 5.6 - - + -
118Y SER* 2.8 44.4 - - - -
119Y VAL* 1.3 77.5 - - - +
121Y ILE* 1.3 60.9 + - - +
122Y PHE* 3.7 10.8 - - + -
138Y CYS* 3.5 2.4 - - - -
139Y LEU* 2.7 53.0 + - + -
141Y ASN* 3.8 13.0 - - + -
211Y LYS* 4.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132X SER* 4.7 0.9 + - - -
134X LYS* 3.2 40.3 + - + +
135X SER* 4.2 3.3 - - - -
120Y PHE* 1.3 72.6 - - - +
122Y PHE* 1.3 65.1 + - - +
123Y PRO* 4.0 4.0 - - - +
136Y VAL* 3.9 9.6 - - + -
137Y VAL 3.6 3.6 - - - +
138Y CYS* 4.2 4.3 - - + +
152Y TRP* 4.0 26.5 - - + -
196Y TYR 4.1 5.2 - - - +
198Y CYS* 4.2 4.0 - - + +
211Y LYS* 3.4 44.4 - - + +
212Y SER 4.4 6.3 - - - +
213Y PHE* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129X LEU* 3.0 61.9 - - + -
130X ALA 3.7 11.0 - - - +
135X SER* 4.1 6.3 - - - -
142X ALA* 3.4 39.0 - - + -
143X LEU* 3.5 7.2 - - - -
186X VAL* 4.9 4.3 - - + -
120Y PHE* 3.7 22.2 - - + -
121Y ILE* 1.3 77.2 - - - +
123Y PRO* 1.3 66.9 - - + +
136Y VAL* 3.0 23.2 - - - +
137Y VAL* 2.7 37.5 + - + +
139Y LEU* 4.1 15.9 - - + -
----------------------------------------------------------
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