Contacts of the strand formed by residues 74 - 78 (chain F) in PDB entry 1XWD
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 LYS 74 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D HIS* 5.3 5.3 - - - -
85D SER* 3.1 26.7 + - - -
86D THR* 3.4 16.3 + - - +
88D TYR* 5.4 0.6 + - - -
49F ILE 3.2 2.2 + - - -
50F GLU* 3.3 37.0 + - + +
51F LEU 3.0 23.7 + - - +
72F LEU* 3.9 1.9 - - - +
73F GLU* 1.3 91.2 - - + +
75F ILE* 1.3 65.5 + - - +
76F GLU* 4.1 1.1 - - + +
98F HIS* 5.8 1.3 - - + -
99F GLU* 3.4 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F LEU* 3.4 9.6 - - + +
53F PHE* 4.5 3.4 - - + -
66F PHE* 3.8 41.3 - - + -
72F LEU* 3.6 27.8 - - + -
74F LYS* 1.3 78.2 - - - +
76F GLU* 1.3 60.3 + - - +
77F ILE* 4.1 18.3 - - + +
91F PHE* 3.8 25.6 - - + -
94F LEU* 4.5 2.5 - - + -
97F LEU* 3.7 21.1 - - + -
99F GLU* 3.0 10.0 + - - +
100F ILE* 3.6 4.0 - - + +
101F ARG* 2.8 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E VAL* 5.2 4.7 - - - +
97E ARG* 4.9 14.5 - - - +
50F GLU* 4.2 8.2 + - - +
51F LEU 2.8 12.4 + - - +
52F ARG* 3.6 36.5 - - + -
53F PHE* 2.9 26.0 + - - -
54F VAL* 3.9 9.6 - - + +
74F LYS* 4.1 1.9 - - + -
75F ILE* 1.3 72.3 - - - +
77F ILE* 1.3 65.3 + - - +
78F SER* 3.8 25.8 + - - +
99F GLU* 5.6 3.0 - - - +
101F ARG* 3.6 38.9 + - + +
103F GLU* 5.4 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F PHE* 3.6 22.9 - - + +
58F LEU* 5.8 1.1 - - + -
61F ILE* 3.4 26.7 - - + -
66F PHE* 5.1 3.8 - - + -
75F ILE* 4.1 12.1 - - + -
76F GLU* 1.3 76.6 - - - +
78F SER* 1.3 59.2 + - - +
80F ASN* 3.7 12.8 - - - +
83F LEU* 3.7 27.6 - - + -
86F ILE* 5.4 1.1 - - + -
91F PHE* 4.2 23.1 - - + -
100F ILE* 6.1 0.2 - - + -
101F ARG 2.7 15.4 + - - +
102F ILE* 3.3 16.1 - - + +
103F GLU 2.9 25.8 + - - +
105F ALA* 6.1 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E THR* 5.5 0.7 - - - +
97E ARG 5.2 3.5 + - - -
53F PHE 2.8 9.9 + - - -
54F VAL* 3.1 31.0 - - - +
76F GLU* 3.8 28.1 + - - -
77F ILE* 1.3 74.8 - - - +
79F GLN* 1.3 76.7 + - - +
80F ASN* 3.0 12.0 + - - +
101F ARG* 5.7 0.2 + - - -
103F GLU* 3.4 16.6 + - - +
104F LYS* 3.8 12.1 + - - -
----------------------------------------------------------
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