Contacts of the strand formed by residues 98 - 103 (chain F) in PDB entry 5IJ7
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 98 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO* 6.6 0.2 - - + -
68B VAL* 4.6 21.8 - - + +
87F PHE* 3.3 7.5 - - - -
88F ASN* 2.8 39.3 + - + +
91F SER* 5.3 2.9 + - - -
96F PRO* 3.4 9.7 + - + +
97F LEU* 1.4 74.9 - - - +
99F PHE* 1.3 64.8 + - - +
109F LEU* 5.0 3.6 - - + -
110F TYR 3.1 16.6 - - - +
111F GLU* 3.9 25.4 - - + +
121F LEU* 4.1 9.2 - - + -
138F TRP* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F VAL* 4.0 16.4 - - + -
86F GLN 3.3 13.5 - - - +
87F PHE* 3.8 24.7 - + + -
88F ASN 4.5 0.2 - - - +
98F VAL* 1.3 75.7 - - - +
100F ALA* 1.3 62.0 + - - +
101F THR* 4.1 4.9 - - - -
109F LEU* 3.5 1.9 - - - -
110F TYR* 2.9 72.5 + + + -
112F CYS* 3.6 32.8 - - - -
118F ILE* 3.8 11.9 - - + -
138F TRP* 4.2 5.2 - - - -
412F ILE* 3.8 25.8 - - + -
420F ILE* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F VAL* 3.4 7.3 - - - +
86F GLN 2.8 28.2 + - - +
99F PHE* 1.3 74.5 - - - +
101F THR* 1.3 67.0 + - - +
107F VAL* 5.1 0.4 - - + -
108F THR 3.3 7.6 - - - +
109F LEU* 4.4 2.5 - - + +
136F CYS* 4.2 8.5 - - - -
138F TRP* 3.6 27.7 - - + +
149F LEU* 3.6 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F GLU* 3.0 32.1 - - - +
82F LEU* 3.4 28.9 - - + -
84F GLY 3.5 4.5 - - - +
85F VAL* 3.5 17.0 - - - +
99F PHE* 4.1 8.0 - - - -
100F ALA* 1.3 76.3 + - - +
102F VAL* 1.3 62.9 + - - +
106F ARG 3.9 0.7 - - - +
107F VAL* 3.4 6.9 - - - +
108F THR* 2.7 38.2 + - - -
110F TYR* 4.0 7.4 - - + -
414F VAL* 3.9 7.6 - - - +
420F ILE* 4.5 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F LEU* 3.5 6.0 - - - -
83F PHE* 2.9 25.3 + - - -
84F GLY* 2.9 41.6 + - - +
101F THR* 1.3 79.8 - - - +
103F GLY* 1.3 58.2 + - - +
106F ARG 3.6 9.0 - - - +
107F VAL* 4.1 4.3 - - + -
133F PHE* 4.0 18.0 - - + +
134F TYR 4.0 0.7 - - - -
135F THR 3.8 28.9 - - - +
136F CYS* 3.8 12.3 - - + -
151F VAL* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F GLU* 5.3 0.6 + - - +
78F HIS* 4.3 5.8 + - - -
81F PRO 3.4 17.9 - - - -
82F LEU* 3.9 9.2 - - - +
83F PHE 4.5 0.4 - - - -
102F VAL* 1.3 75.1 - - - +
104F SER* 1.4 66.8 + - - -
106F ARG* 2.9 31.8 + - - +
132F ASN* 4.8 0.4 - - - -
133F PHE 3.9 9.5 + - - -
----------------------------------------------------------
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