Contacts of the strand formed by residues 116 - 121 (chain I) in PDB entry 2IAN
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 ALA 116 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I ASP* 3.0 8.9 + - - +
115I PRO* 1.3 74.6 - - - +
117I VAL* 1.3 63.5 + - - +
118I TYR* 3.3 38.8 - - + +
132I LEU 3.7 0.2 - - - +
133I PHE* 3.2 6.5 - - - -
134I THR* 3.1 30.8 + - - +
135I ASP* 5.8 0.2 - - + -
194I THR* 3.6 4.4 - - - +
195I PHE* 3.6 21.3 - - + +
133J HIS* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ALA* 1.3 78.0 - - - +
118I TYR* 1.3 65.0 + - - +
131I CYS* 4.2 14.1 - - + -
132I LEU 3.3 7.2 - - - +
133I PHE* 3.6 20.6 - - + -
181I CYS* 3.6 33.6 - - + +
185I PHE* 4.0 19.7 - - + -
194I THR* 4.0 5.3 - - + +
195I PHE 3.2 6.7 + - - +
196I PHE* 4.0 25.4 - - + -
197I PRO* 3.2 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I ASP 4.9 1.2 + - - -
116I ALA* 3.3 25.6 - - + +
117I VAL* 1.3 81.6 - - - +
119I GLN* 1.3 60.2 + - - +
120I LEU* 3.3 11.0 - - + +
131I CYS* 3.4 3.2 - - - -
132I LEU* 2.8 43.3 + - + +
134I THR* 3.8 28.3 - - + -
135I ASP* 5.0 3.0 + - - -
181I CYS* 4.7 0.4 - - - -
195I PHE* 3.7 24.2 - + - -
197I PRO* 4.0 4.7 - - + -
127J SER* 3.3 17.9 - - - +
129J ALA* 3.9 9.6 - - + -
130J GLU* 3.5 47.7 - - + +
133J HIS* 3.7 23.0 - - - -
134J THR* 4.0 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I VAL 4.4 0.4 + - - -
118I TYR* 1.3 74.3 - - - +
120I LEU* 1.3 64.3 + - - +
121I ARG* 4.5 21.9 + - + +
129I SER* 3.4 28.2 + - - +
130I VAL 3.4 6.7 - - - +
180I ALA* 5.8 0.7 - - - -
181I CYS* 3.5 29.1 + - + +
197I PRO* 5.0 4.9 - - - +
127J SER* 3.3 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I TYR* 3.3 28.3 - - + +
119I GLN* 1.3 78.4 - - - +
121I ARG* 1.3 61.8 + - - +
129I SER* 3.2 4.4 - - - -
130I VAL* 2.8 40.0 + - + +
132I LEU* 3.7 21.5 - - + -
124J PHE* 3.3 18.7 - - + +
125J GLU 3.2 24.5 - - - +
126J PRO* 4.3 5.8 - - + -
127J SER* 4.5 2.5 - - - +
130J GLU* 6.1 0.9 - - - +
138J THR 3.5 21.5 - - - +
140J VAL* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I GLN* 4.5 17.1 + - + +
120I LEU* 1.3 74.8 - - - +
122I ASP* 1.3 70.5 + - - +
123I SER 3.5 0.2 + - - -
126I SER* 3.4 36.3 + - - +
128I LYS 3.7 2.0 - - - -
129I SER* 4.1 13.0 - - - -
124J PHE* 3.6 3.1 - - - -
125J GLU* 3.0 29.2 + - - +
----------------------------------------------------------
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