Contacts of the strand formed by residues 116 - 122 (chain N) 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 N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N ASP 3.2 4.2 + - - +
115N PRO* 1.3 74.6 - - - +
117N VAL* 1.3 61.6 + - - +
118N TYR* 3.4 41.5 - - + +
132N LEU 4.3 0.9 - - - -
133N PHE* 2.8 27.2 - - - -
134N THR 3.1 16.5 + - - +
194N THR* 3.8 1.8 - - - -
195N PHE* 3.3 23.1 - - + +
133O HIS* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116N ALA* 1.3 80.7 - - - +
118N TYR* 1.3 63.0 + - - +
131N CYS* 4.2 13.2 - - + -
132N LEU 3.5 6.1 - - - +
133N PHE* 3.7 21.1 - - + -
181N CYS* 3.5 36.2 - - + +
185N PHE* 4.3 18.2 - - + -
190N ILE* 5.9 1.6 - - + -
194N THR* 4.1 7.6 - - + -
195N PHE 3.2 4.5 + - - +
196N PHE* 3.8 23.3 - - + -
197N PRO* 3.1 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N ASP 5.1 1.7 + - - -
116N ALA* 3.4 26.1 - - + +
117N VAL* 1.3 74.6 - - - +
119N GLN* 1.3 60.1 + - - +
120N LEU* 4.0 9.6 - - + -
131N CYS* 3.1 8.3 - - - +
132N LEU* 2.7 36.9 + - + +
134N THR* 3.6 32.1 - - + -
135N ASP* 5.1 2.1 + - - -
181N CYS* 4.3 3.8 - - - -
195N PHE* 4.3 9.2 - + - -
197N PRO* 4.0 7.9 - - + -
127O SER* 3.3 24.9 - - - +
129O ALA* 3.6 20.0 - - + -
130O GLU* 3.3 36.3 - - + -
133O HIS* 3.9 10.7 - - - +
134O THR* 3.6 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N VAL 4.4 0.2 + - - -
118N TYR* 1.3 72.9 - - - +
120N LEU* 1.3 69.7 + - - +
121N ARG* 4.2 27.8 + - + +
127N ASP 5.2 0.8 + - - -
129N SER* 4.2 24.9 + - - +
130N VAL 3.6 9.9 - - - +
131N CYS* 5.4 0.6 - - - -
179N PHE 5.9 1.0 + - - -
180N ALA* 6.4 0.2 - - - +
181N CYS* 4.1 18.2 - - - -
197N PRO* 4.5 9.2 - - + +
127O SER* 3.2 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N TYR* 4.3 9.4 - - + +
119N GLN* 1.3 79.5 - - - +
121N ARG* 1.3 65.1 + - - +
128N LYS 3.9 1.2 - - - +
129N SER* 4.6 0.2 - - - -
130N VAL* 3.0 38.7 + - + +
132N LEU* 3.5 36.8 - - + -
124O PHE* 3.2 29.8 - - + +
125O GLU 3.2 15.9 - - - +
126O PRO* 4.1 6.3 - - + -
127O SER* 4.2 3.6 - - - +
130O GLU* 5.8 1.1 - - - +
138O THR 3.1 27.4 - - - +
140O VAL* 3.9 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119N GLN* 4.2 26.6 + - + +
120N LEU* 1.3 79.4 - - - +
122N ASP* 1.3 67.9 + - - +
126N SER* 3.4 41.2 + - - +
127N ASP* 4.2 14.2 + - - +
128N LYS 4.0 1.6 - - - +
124O PHE* 3.1 6.2 - - - -
125O GLU* 2.9 32.8 + - - +
126O PRO 5.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N ARG* 1.3 78.8 - - - +
123N SER* 1.3 67.1 + - - +
124N LYS* 2.7 60.9 + - - +
125N SER 4.3 3.7 - - - +
126N SER* 4.3 6.4 + - - +
128N LYS* 3.4 37.6 + - + +
122O ALA* 3.9 17.2 - - - +
123O VAL 3.3 12.2 + - - +
124O PHE* 3.2 16.3 - - + -
125O GLU* 5.1 0.8 - - - -
----------------------------------------------------------
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