Contacts of the strand formed by residues 113 - 118 (chain H) in PDB entry 5IYB
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 113 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ILE* 2.6 27.2 + - - +
100H GLU* 3.3 18.4 - - - +
101H GLY* 4.9 0.6 - - - +
112H LEU* 1.3 73.1 - - - +
114H ALA* 1.3 57.9 + - - +
115H TYR* 4.1 9.7 - - - -
124H ARG* 4.4 13.0 - - - -
125H LEU 3.3 10.3 - - - -
126H GLN* 3.0 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H VAL* 4.7 7.2 - - + -
98H ARG 4.0 7.0 - - - +
99H ILE* 4.0 11.0 - - + +
112H LEU* 3.3 16.7 - - + +
113H SER* 1.3 73.6 - - - +
115H TYR* 1.3 61.0 + - - +
116H VAL* 4.5 6.4 + - + +
124H ARG* 3.7 3.3 - - - +
125H LEU* 3.1 40.3 + - + +
130H ASN* 4.6 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A HIS 5.2 0.7 + - - -
621A ILE* 4.5 26.0 + - + +
623A PRO* 4.8 11.0 - - + -
96H VAL* 3.1 20.8 - - - +
97H TYR* 3.2 31.1 + + + -
98H ARG* 3.1 54.4 + - + +
99H ILE 4.6 0.4 - - - -
100H GLU* 4.4 14.0 + - + +
113H SER* 4.1 19.0 - - - -
114H ALA* 1.3 71.6 - - - +
116H VAL* 1.3 62.6 + - - +
123H MET 3.5 5.8 - - - +
124H ARG* 3.3 48.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ILE* 6.3 1.8 - - + -
95H LYS 3.3 23.6 - - - +
96H VAL* 4.0 16.2 - - + -
97H TYR* 3.8 5.8 - - - -
114H ALA* 4.9 7.2 - - + +
115H TYR* 1.3 81.1 - - - +
117H SER* 1.3 63.4 + - - +
118H TYR* 3.3 34.8 - - + +
121H LEU 3.9 0.2 - - - +
122H LEU* 3.5 3.3 - - - -
123H MET* 2.9 52.8 + - + +
125H LEU* 6.0 3.4 - - + +
141H VAL* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 3.1 30.1 + - - -
94H GLY* 3.2 2.6 - - - -
95H LYS* 2.9 37.6 + - - +
97H TYR* 3.6 24.0 - - - -
116H VAL* 1.3 73.6 - - - +
118H TYR* 1.3 62.5 + - - +
119H GLY 3.6 4.0 + - - -
120H GLY 3.5 10.2 + - - -
121H LEU 3.6 3.6 - - - -
122H LEU* 3.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ALA* 4.1 9.7 - - - +
41H LEU* 4.3 2.2 - - + -
60H ILE* 5.1 2.6 - - - +
92H MET* 4.0 34.9 - - + +
93H TYR 3.4 29.4 - - - +
94H GLY* 3.4 10.1 - - - -
116H VAL* 3.3 27.6 - - + +
117H SER* 1.3 70.4 + - - +
119H GLY* 1.3 56.9 + - - +
120H GLY 3.1 2.9 - - - -
121H LEU* 2.8 50.8 + - + +
123H MET* 3.2 35.6 - - + +
141H VAL* 3.6 17.5 - - + +
143H LEU* 3.4 35.3 - - + +
----------------------------------------------------------
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