Contacts of the strand formed by residues 119 - 126 (chain B) in PDB entry 4IYM
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 119 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLN 3.5 0.5 + - - -
118B LYS* 1.3 75.3 - - - +
120B GLU* 1.3 68.4 + - - +
133B SER* 2.5 38.7 + - - -
134B ILE* 3.4 12.0 - - - +
135B ARG* 4.1 15.7 + - - +
119C SER 3.6 0.2 - - - +
120C GLU* 3.4 9.0 - - - +
121C PHE* 2.9 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A TYR 4.7 0.9 - - - +
446A HIS* 4.1 16.5 + - + -
464A THR* 4.4 14.8 + - - +
119B SER* 1.3 84.0 - - - +
121B PHE* 1.3 60.9 + - - +
132B TYR* 3.2 5.2 - - - +
133B SER* 3.0 35.2 + - - +
115C HIS* 4.2 8.5 - - - -
118C LYS* 3.1 49.7 + - + +
119C SER 3.3 5.4 - - - +
121C PHE* 4.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A HIS* 4.7 0.2 - - - -
120B GLU* 1.3 76.1 - - - +
122B THR* 1.3 65.8 + - - +
123B GLU* 3.6 23.1 - - + -
130B ASP* 4.0 23.6 - - + -
131B MSE 3.8 1.6 - - - -
132B TYR* 3.5 36.6 - + + -
117C GLN 4.7 0.5 - - - +
118C LYS* 3.4 8.6 - - - -
119C SER* 2.7 47.4 + - - +
120C GLU 4.5 6.3 - - - +
121C PHE* 4.2 7.4 - + + -
132C TYR* 3.4 37.7 - + - -
133C SER 3.7 15.7 - - - +
134C ILE* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A TYR* 3.6 30.0 - - + +
446A HIS* 2.8 30.6 + - - -
121B PHE* 1.3 80.6 + - - +
123B GLU* 1.3 70.9 + - - +
125B ALA* 3.9 12.8 - - + +
130B ASP* 3.5 2.8 - - - -
131B MSE 2.8 40.1 + - - -
60C PRO* 4.6 9.0 - - + -
114C PRO 4.5 2.8 + - - +
117C GLN 6.0 0.4 - - - -
118C LYS* 4.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 3.6 10.2 - - + -
122B THR* 1.3 76.3 - - - +
124B GLY* 1.3 69.4 + - - +
125B ALA 3.5 0.3 + - - -
130B ASP* 3.3 17.1 - - - +
60C PRO* 4.8 6.2 - - - +
134C ILE* 3.6 34.2 - - + +
135C ARG 5.5 0.2 - - - +
136C GLN* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLU* 1.3 77.5 - - - +
125B ALA* 1.3 66.8 + - - +
126B GLY 3.0 14.3 + - - +
128B GLY* 5.3 1.8 - - - -
129B ILE 3.0 9.7 + - - -
130B ASP* 3.0 13.9 + - - -
57C ALA 5.6 0.7 - - - +
59C ASN* 3.4 18.9 - - - +
60C PRO* 3.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.8 25.3 - - + +
445A TYR* 3.7 23.3 + - - +
122B THR* 3.9 7.1 + - + +
123B GLU 3.3 4.0 + - - -
124B GLY* 1.3 75.9 - - - +
126B GLY* 1.3 57.7 + - - +
129B ILE* 3.0 7.7 + - + +
131B MSE 3.9 32.1 - - + +
59C ASN* 3.4 19.1 + - - +
60C PRO* 4.5 1.8 - - - -
61C GLN* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY* 3.2 17.2 - - - +
125B ALA* 1.3 77.8 - - - +
127B PRO* 1.4 75.0 - - - +
128B GLY 3.2 1.7 + - - -
129B ILE* 3.1 30.3 + - - +
59C ASN* 4.7 6.7 - - - -
----------------------------------------------------------
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