Contacts of the strand formed by residues 113 - 124 (chain A) in PDB entry 3IAY
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 ILE 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 4.0 14.1 - - + -
111A TYR 3.8 0.2 + - - -
112A ASP* 1.3 76.0 - - - +
114A SER* 1.3 61.0 + - - +
115A PHE* 4.1 10.7 - - + -
143A THR* 4.1 11.7 - - + -
149A VAL* 4.1 26.0 - - + -
270A ILE 3.7 0.9 - - - +
271A THR* 3.4 1.3 - - - -
272A LEU* 2.7 57.1 + - + +
277A TYR* 3.5 38.8 - - + +
291A LEU* 4.1 17.3 - - + -
293A VAL* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 4.1 4.9 - - - +
113A ILE* 1.3 70.5 - - - +
115A PHE* 1.3 61.7 + - - +
143A THR* 3.4 24.6 - - - +
144A SER 4.2 1.2 + - - -
269A TRP* 3.7 7.6 - - - -
270A ILE 3.3 5.6 - - - -
271A THR* 2.5 32.7 + - - +
309A TRP* 3.7 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.1 12.8 - - + -
114A SER* 1.3 77.0 - - - +
116A GLN* 1.3 62.6 + - - +
117A GLN* 3.5 18.0 + - + -
139A PHE* 4.3 12.6 - - + -
140A PHE 4.3 3.4 - - - -
141A GLY* 3.8 27.1 - - - -
142A VAL 3.3 19.7 - - - +
143A THR* 3.9 1.8 - - + +
149A VAL* 3.9 23.1 - - + -
151A CYS* 3.7 21.8 - - + -
269A TRP* 3.3 8.0 - - - -
270A ILE* 3.0 66.7 + - + +
272A LEU* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 1.3 71.9 - - - +
117A GLN* 1.3 65.6 + - - +
118A ILE* 3.6 8.9 + - + +
141A GLY* 3.1 20.8 - - - -
142A VAL* 2.8 12.8 + - - +
267A MET* 3.1 53.6 + - - +
268A SER 3.4 5.8 - - - +
269A TRP* 3.5 16.0 - - + +
312A THR* 3.4 16.4 - - - +
313A ALA* 2.6 47.3 + - + +
315A LEU* 4.3 5.3 - - + +
538A THR* 4.3 1.0 - - - +
542A ARG* 3.6 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 3.5 21.9 + - + -
116A GLN* 1.3 71.6 - - - +
118A ILE* 1.3 62.6 + - - +
119A ASP* 3.7 13.5 + - - +
120A ALA* 4.8 0.8 - - - +
139A PHE* 3.5 28.8 - - + -
140A PHE 3.4 8.7 - - - +
259A MET* 4.3 5.1 - - - +
264A ILE* 3.3 7.0 - - - +
265A VAL 2.7 27.7 - - - +
266A GLY* 4.1 1.6 - - - -
267A MET* 3.2 22.2 + - - +
268A SER* 2.8 25.4 + - - +
270A ILE* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 4.0 13.2 - - + +
117A GLN* 1.3 80.0 - - - +
119A ASP* 1.3 69.7 + - + +
140A PHE 2.8 17.2 + - - +
141A GLY* 4.8 1.8 - - - -
267A MET* 3.7 30.3 - - + +
315A LEU* 4.2 20.9 - - + -
396A ASP* 3.5 44.2 - - + +
428A ARG* 4.1 2.0 - - - +
458A GLY 3.9 16.2 - - - +
460A LEU* 3.3 32.0 - - + +
547A PRO* 5.5 0.7 - - - +
548A PHE* 4.2 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 3.7 7.8 + - - +
118A ILE* 1.3 88.3 - - + +
120A ALA* 1.3 80.5 + - - +
139A PHE* 3.4 1.7 - - - -
140A PHE* 2.9 29.9 + - + +
458A GLY* 4.8 19.6 + - - -
459A ARG 4.5 7.6 - - - +
460A LEU* 4.0 16.0 - - + +
547A PRO* 4.4 11.1 - - - +
549A SER* 3.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 4.8 0.9 - - - +
119A ASP* 1.3 92.2 + - - +
121A GLU* 1.3 63.7 + - - +
137A VAL* 3.7 11.7 - - + -
138A ARG 3.1 9.9 - - - +
139A PHE* 3.5 32.5 - - + -
140A PHE* 4.9 1.1 - - - -
255A THR* 4.1 16.8 - - + +
259A MET* 5.1 4.0 - - - -
547A PRO* 5.8 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 6.1 0.2 - - - +
120A ALA* 1.3 78.6 - - - +
122A GLN* 1.3 71.7 + - - +
123A SER* 3.6 2.1 + - - -
137A VAL* 3.6 2.4 - - - -
138A ARG* 2.8 38.4 + - + +
140A PHE* 4.3 16.2 - - + -
255A THR* 3.9 7.2 - - - -
429A LEU* 3.1 24.1 - - - +
455A ASN* 5.8 0.5 - - - +
457A ASP* 3.0 37.8 - - - +
458A GLY 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 1.3 81.4 - - - +
123A SER* 1.3 67.2 + - - +
124A VAL* 6.2 1.4 - - - +
135A THR* 3.9 10.9 + - + +
136A VAL 3.5 6.1 - - - -
137A VAL* 4.6 0.9 - - - +
221A PRO* 3.6 25.8 - - - +
222A HIS* 4.7 7.7 - - - +
254A TYR* 3.7 38.9 - - + +
255A THR* 3.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.6 5.3 + - - -
122A GLN* 1.3 80.2 - - - +
124A VAL* 1.3 70.0 + - - +
135A THR* 3.4 5.7 - - - +
136A VAL* 2.7 34.2 + - - +
138A ARG* 3.2 44.9 + - - -
429A LEU* 5.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLN* 6.2 1.1 - - - +
123A SER* 1.3 79.2 + - - +
125A LEU* 1.3 69.5 + - - +
126A ASN* 3.8 4.0 + - - +
134A SER* 3.6 21.8 - - - +
135A THR* 3.6 19.7 - - + +
136A VAL* 5.0 0.2 - - - -
138A ARG* 3.6 14.9 + - - -
220A TYR* 6.2 0.7 - - + -
----------------------------------------------------------
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