Contacts of the strand formed by residues 55 - 60 (chain A) in PDB entry 3I54
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 55 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 5.0 0.4 - - + -
50A ILE* 4.0 22.4 - - + -
54A LYS* 1.3 80.0 - - - +
56A LYS* 1.3 63.9 + - - +
57A ILE* 4.1 8.4 + - + -
70A THR 4.2 0.2 - - - +
71A ILE* 3.4 5.5 - - - +
72A MET* 2.8 35.5 + - + +
78A PHE* 4.0 22.0 - - + -
93A ALA* 3.9 29.2 - - + -
94A THR 3.4 11.2 - - - +
95A THR* 4.2 12.6 - - + -
96A ILE* 4.9 0.4 - - - -
99A VAL* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 1.3 73.9 - - - +
57A ILE* 1.3 61.6 + - - +
58A GLY* 4.0 1.0 + - - +
66A GLU* 5.4 5.8 + - - -
68A LEU* 3.9 28.4 - - + +
71A ILE* 3.4 25.4 - - + -
92A SER 3.6 1.0 - - - +
93A ALA* 3.5 2.9 - - - -
94A THR* 2.8 63.3 + - - +
95A THR 5.2 0.7 - - - -
96A ILE* 3.6 20.9 - - + +
179A GLU* 2.7 30.4 + - - +
182A GLN* 5.1 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.1 8.5 - - + -
56A LYS* 1.3 75.2 - - - +
58A GLY* 1.3 58.9 + - - +
68A LEU* 3.2 6.9 - - - +
69A LEU* 2.8 34.0 + - + -
70A THR* 3.0 33.5 + - + +
72A MET* 4.2 11.2 - - + -
78A PHE* 4.2 15.5 - - + -
91A SER* 3.1 30.5 - - - +
92A SER 3.3 2.5 - - - +
93A ALA* 3.9 27.4 - - + -
301A CMP 3.3 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 4.4 0.2 - - - +
56A LYS* 4.0 2.1 + - - -
57A ILE* 1.3 74.8 - - - +
59A ARG* 1.3 61.7 + - - -
66A GLU* 5.6 4.0 - - - -
67A ASN 3.3 11.0 - - - -
68A LEU* 3.9 9.9 - - - -
69A LEU* 4.7 2.0 - - - -
91A SER* 3.2 5.7 - - - -
92A SER* 2.9 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 3.4 21.7 + - - +
58A GLY* 1.3 80.0 - - - +
60A ARG* 1.3 62.8 + - - +
61A ALA 4.0 0.5 + - - -
66A GLU* 3.2 7.1 - - - +
67A ASN* 3.0 40.5 + - - +
69A LEU* 4.0 26.2 - - + +
90A THR* 3.4 43.2 + - - +
91A SER* 3.7 2.9 - - - -
92A SER* 5.1 0.2 - - - -
135B ASN* 4.5 9.4 + - - +
136B ASN* 2.9 30.9 + - - +
139B ALA* 3.5 32.0 - - - +
143B PHE* 4.2 3.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 3.3 17.8 + - - +
59A ARG* 1.3 74.8 - - - +
61A ALA* 1.3 66.4 + - - +
62A PRO* 4.7 0.3 - - - +
64A GLY* 4.8 6.5 - - - +
65A ARG 3.2 8.5 - - - +
66A GLU* 4.4 9.9 - - + +
92A SER* 5.7 0.4 + - - -
143B PHE* 4.7 2.0 - - - -
----------------------------------------------------------
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