Contacts of the helix formed by residues 93 - 101 (chain I) in PDB entry 1XFB
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 PRO 93 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I LEU 6.1 0.4 - - - +
85I TYR 6.4 0.2 - - - -
86I GLN 3.6 2.7 - - - +
87I LYS* 3.6 23.1 - - + -
91I GLY 3.6 7.2 - - - +
92I VAL* 1.3 90.2 - - + +
94I PHE* 1.3 66.5 + - - +
95I VAL* 4.2 6.3 - - + +
96I ARG* 2.8 50.0 + - + +
97I THR* 3.1 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I ARG* 3.4 29.6 - - + -
60I ARG* 4.1 7.6 - - + -
61I GLN* 3.8 24.5 - - + -
64I PHE* 3.3 35.4 - + + -
79I PHE* 3.8 10.3 - - + -
83I THR* 3.9 7.9 - - + +
86I GLN* 3.1 49.8 + - + +
87I LYS 3.8 10.8 - - - -
88I ASP* 3.7 27.6 - - + -
92I VAL 3.2 2.5 + - - -
93I PRO* 1.3 71.3 - - - +
95I VAL* 1.3 63.8 + - - +
97I THR* 3.3 7.5 + - - -
98I ILE* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE* 4.2 12.1 - - + -
84I LEU* 3.2 51.6 - - + +
86I GLN 5.9 0.2 - - - +
93I PRO* 3.0 6.2 - - + -
94I PHE* 1.3 79.0 - - - +
96I ARG* 1.3 63.3 + - - +
98I ILE* 3.4 1.4 + - - +
99I GLN* 2.8 52.0 + - + +
105I VAL* 4.0 13.9 - - + -
141I ASP 3.8 19.7 - - - +
142I GLY* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.3 27.2 - - - +
243A LYS* 2.8 25.0 + - - +
244A TYR* 3.7 6.9 - - - +
245A THR* 4.3 1.6 + - - +
248A GLU* 2.4 44.5 + - - -
92I VAL* 4.1 11.9 - - + +
93I PRO* 2.8 41.3 + - + +
95I VAL* 1.3 79.2 - - - +
97I THR* 1.3 58.6 + - - +
99I GLN* 3.1 10.1 + - - +
100I ASP* 2.8 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I PHE* 3.6 24.9 - - - +
65I SER* 5.6 1.1 - - - -
88I ASP* 4.4 7.8 + - - +
92I VAL* 3.7 15.2 + - - +
93I PRO 3.1 8.8 + - - -
94I PHE* 3.5 13.0 - - - -
96I ARG* 1.3 78.2 - - - +
98I ILE* 1.3 68.5 + - + +
100I ASP* 3.0 19.3 + - - +
101I LYS* 3.2 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I PHE* 3.5 45.1 - - + +
77I VAL* 3.9 23.1 - - + -
79I PHE* 4.1 11.4 - - + -
94I PHE 3.1 20.6 + - - +
95I VAL 3.9 2.7 - - - +
97I THR* 1.3 79.3 - - - +
99I GLN* 1.3 63.5 + - - +
101I LYS* 3.2 13.2 + - + +
103I ILE* 3.2 55.3 + - + +
104I VAL 4.2 1.3 - - - +
105I VAL* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 6.1 1.0 - - - +
241A PRO* 4.1 12.1 - - - +
242A ILE* 3.1 46.3 - - + +
95I VAL* 2.8 37.2 + - - +
96I ARG* 3.3 11.0 - - - +
98I ILE* 1.3 77.0 - - - +
100I ASP* 1.3 58.2 + - - +
102I GLY* 2.8 21.8 + - - -
103I ILE 3.9 7.9 - - - +
105I VAL* 3.7 15.2 - - + +
142I GLY* 3.7 30.5 + - - -
144I ASP* 5.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 4.9 5.1 - - - +
200A LYS* 4.0 30.6 - - + +
242A ILE* 3.7 17.7 - - - +
244A TYR* 3.8 13.8 + - - -
71I LYS* 5.4 1.2 + - - -
96I ARG* 2.8 40.4 + - - +
97I THR* 3.0 10.5 + - - +
99I GLN* 1.3 67.7 - - - +
101I LYS* 1.3 58.4 + - + +
102I GLY* 3.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I PHE 4.4 3.8 - - - -
66I ALA 3.0 28.7 + - - -
67I ASP* 3.5 10.4 - - - +
68I ASP* 3.4 24.7 + - - +
70I VAL* 4.0 21.1 - - + -
71I LYS* 3.3 39.3 - - + +
97I THR* 3.2 27.8 + - - +
98I ILE* 3.7 9.6 - - + +
99I GLN 3.2 0.8 - - - -
100I ASP* 1.3 76.7 - - + +
102I GLY* 1.3 60.5 + - - +
103I ILE* 3.2 13.4 + - + +
----------------------------------------------------------
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