Contacts of the strand formed by residues 128 - 134 (chain F) in PDB entry 4KYI
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 VAL 128 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F GLN 3.4 7.9 + - - +
96F ALA* 3.4 2.9 - - - +
97F ALA 3.1 23.3 + - - +
126F ASN 5.1 2.5 - - - +
127F ILE* 1.3 81.7 - - - +
129F ILE* 1.3 65.9 + - - +
130F ALA 3.7 0.5 + - - -
159F LEU* 4.5 11.4 - - + -
178F ILE* 4.0 21.4 - - + +
181F LYS* 3.5 48.7 - - + +
182F LEU* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ALA* 3.6 5.8 - - + +
99F VAL* 4.3 7.9 - - + -
116F VAL* 4.6 7.9 - - + +
119F LEU* 3.7 48.2 - - + -
120F GLN* 4.4 18.2 - - + -
127F ILE* 3.7 29.0 + - + -
128F VAL* 1.3 72.2 - - - +
130F ALA* 1.3 72.1 + - - +
157F SER 4.6 2.6 + - - +
158F LEU* 3.8 28.5 - - + -
159F LEU* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ALA 2.8 15.1 + - - +
98F ILE* 4.3 7.4 - - + -
99F VAL* 3.3 21.7 + - - +
116F VAL* 5.7 0.2 - - - +
128F VAL 3.7 0.6 + - - -
129F ILE* 1.3 84.4 - - - +
131F LEU* 1.3 62.1 + - - +
158F LEU* 5.3 1.1 - - - +
159F LEU* 3.2 20.0 - - + +
174F ILE* 4.5 11.2 - - + -
178F ILE* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F VAL* 3.3 27.6 - - + +
101F TYR* 3.8 18.2 - - + -
109F PHE* 4.3 20.2 - - + -
112F ALA* 4.5 12.1 - - + -
116F VAL* 5.3 4.5 - - + -
130F ALA* 1.3 76.2 - - - +
132F ALA* 1.3 64.1 + - - +
149F ALA 4.6 8.7 - - - +
152F TYR* 4.7 4.9 - - + -
153F ALA* 5.3 0.2 - - + -
158F LEU* 4.2 24.9 - - + -
159F LEU 3.0 7.7 + - - -
160F PHE* 3.6 33.0 - - + +
161F MET* 2.8 30.1 + - - +
174F ILE* 3.9 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 4.8 3.1 - - + -
98F ILE* 4.4 5.6 - - + -
99F VAL 3.0 13.6 + - - +
100F VAL* 3.6 18.3 - - + -
101F TYR* 2.8 36.3 + - - +
131F LEU* 1.3 76.4 - - - +
133F GLY* 1.3 59.9 + - - +
134F ASN 3.4 0.7 + - - -
161F MET 3.6 3.4 - - - -
163F THR* 3.6 18.6 - - + +
174F ILE* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F TYR* 3.4 33.4 - - - -
103F ILE* 3.8 9.3 - - - +
132F ALA* 1.3 70.0 - - - +
134F ASN* 1.3 67.1 + - - +
136F ALA* 3.9 5.7 - - - +
160F PHE* 4.9 0.4 - - - -
161F MET 3.3 13.2 + - - -
162F GLU* 4.1 6.9 - - - +
163F THR* 3.1 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F VAL 2.8 29.1 + - - +
33F GLY 3.4 12.6 + - - -
37F LEU* 3.9 8.5 - - - +
100F VAL* 3.9 13.0 - - + -
101F TYR 3.0 10.1 + - - +
102F ASP* 4.4 1.6 - - - -
103F ILE* 3.5 17.2 + - - +
132F ALA 3.4 1.8 + - - -
133F GLY* 1.3 78.7 - - - +
135F LYS* 1.3 77.2 + - + +
136F ALA 3.1 0.8 + - - -
163F THR* 3.2 15.1 + - - +
164F SER* 3.3 13.2 + - - -
165F ALA 3.5 2.9 + - - -
301F GNP 2.8 38.0 + - - +
----------------------------------------------------------
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