Contacts of the strand formed by residues 74 - 79 (chain L) 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 ILE 74 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L LYS* 3.7 11.9 + - - -
29L GLY 3.5 2.7 - - - +
31L LEU* 4.5 16.8 - - + +
70L VAL* 2.9 39.8 + - + +
71L LYS 4.1 0.2 - - - +
72L LYS 3.8 0.6 - - - -
73L CYS* 1.3 87.3 - - - +
75L GLY* 1.3 59.9 + - - +
76L GLY 3.5 23.3 - - - +
77L VAL* 4.1 7.9 - - + -
103L ILE* 3.6 34.9 - - + +
300L PHE* 4.2 18.6 - - + -
306L LEU* 4.7 2.7 - - + -
328L PHE* 4.7 4.5 - - + -
332L ALA* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L ARG 4.3 1.9 - - - +
23L ILE* 3.6 28.1 - - - -
28L LYS* 3.8 20.9 - - - +
29L GLY 2.7 12.5 + - - -
74L ILE* 1.3 74.3 - - - +
76L GLY* 1.3 54.0 + - - -
102L GLY 4.9 0.3 - - - +
103L ILE* 3.6 3.5 - - - +
104L VAL* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L ILE* 4.4 7.1 - - - +
29L GLY 3.4 3.4 + - - -
30L ILE* 3.3 8.8 - - - -
31L LEU 2.9 24.1 + - - -
74L ILE* 3.4 6.4 - - - +
75L GLY* 1.3 80.7 - - - +
77L VAL* 1.3 65.4 + - - -
103L ILE* 3.5 2.2 - - - -
104L VAL* 3.2 15.0 - - - -
145L PHE* 4.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L LEU* 3.3 23.6 - - + +
33L ALA* 4.8 0.7 - - + -
64L PHE* 3.6 31.0 - - + -
74L ILE* 4.1 8.7 - - + -
76L GLY* 1.3 79.9 - - - +
78L ILE* 1.3 67.7 + - - +
79L PHE* 3.5 20.9 - - + -
98L ILE* 3.9 15.7 - - + -
103L ILE* 3.6 20.9 - - + -
104L VAL 2.9 8.0 + - - +
106L GLY 2.9 23.6 + - - -
145L PHE* 3.9 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ILE* 3.6 27.6 - - + -
31L LEU 2.8 11.6 + - - +
32L ALA* 4.1 9.2 - - + -
33L ALA* 3.0 31.0 + - - +
34L ASP* 3.6 22.9 - - + +
77L VAL* 1.3 71.8 - - - +
79L PHE* 1.3 63.3 + - - +
106L GLY 3.5 5.2 - - - +
107L ILE 4.3 3.1 - - - +
108L LYS 4.1 11.2 - - - +
145L PHE* 3.6 15.0 - - + -
147L LYS* 4.0 28.5 - - + +
186L ILE* 4.1 13.5 - - + -
230L LYS* 4.1 3.4 - - - +
301L SER* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L ALA* 4.3 2.9 - - - -
34L ASP* 3.7 5.2 - - - +
64L PHE* 3.7 29.4 - + - -
77L VAL* 3.5 30.1 - - + -
78L ILE* 1.3 74.5 - - - +
80L PHE* 1.3 64.4 + - - +
83L THR* 3.5 21.8 - - + -
84L LEU* 3.7 24.2 - - + -
94L PHE* 3.8 20.0 - - + -
95L VAL* 4.2 11.9 - - + -
98L ILE* 4.1 18.2 - - + -
105L VAL* 3.6 24.2 - - + -
106L GLY 2.6 19.0 + - - +
107L ILE* 3.4 4.3 - - + -
108L LYS 3.2 24.4 + - - -
----------------------------------------------------------
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