Contacts of the strand formed by residues 55 - 62 (chain A) in PDB entry 5ITY
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 GLU 55 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.7 3.4 - - - +
51A ALA* 3.3 6.4 - - - +
52A ARG* 2.8 31.3 + - - +
53A GLY 3.1 1.6 - - - +
54A LYS* 1.3 84.5 - - - +
56A LEU* 1.3 63.2 + - - +
76A VAL* 3.5 11.6 - - + +
77A PHE 3.4 8.3 - - - +
78A ARG* 3.0 34.8 + - + -
129A TRP* 3.4 27.2 - - + +
130A GLN* 2.8 29.9 + - - +
133A ARG* 3.4 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.8 15.7 - - + +
10A ALA* 3.8 17.7 - - + +
11A SER* 3.5 36.1 - - - +
14A VAL* 5.1 0.7 - - + -
49A ALA* 4.5 1.3 - - + -
50A SER 3.4 10.3 - - - +
51A ALA* 4.9 0.4 - - - -
55A GLU* 1.3 76.6 - - - +
57A ARG* 1.3 75.3 + - - +
58A LEU* 4.0 12.8 - - + +
75A LEU 3.6 0.2 - - - +
76A VAL* 3.3 2.9 - - - +
77A PHE* 2.8 48.4 + - + +
79A PHE* 4.2 3.6 - - + -
85A PHE* 3.9 28.5 - - + -
129A TRP* 4.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.1 6.4 - - - +
50A SER* 2.7 44.2 + - - +
56A LEU* 1.3 76.6 - - - +
58A LEU* 1.3 69.2 + - - +
59A ILE* 4.0 16.1 + - + +
74A ALA* 4.1 7.9 - - + -
75A LEU 3.2 9.4 - - - +
76A VAL* 4.0 2.9 - - + -
127A GLY* 2.6 48.2 + - - -
128A LYS* 4.6 0.4 - - - +
129A TRP* 3.3 61.6 - - + +
140B GLU* 6.3 1.2 - - - +
143B GLN* 6.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.7 21.5 - - + -
47A ILE* 3.7 29.2 - - + -
48A SER 3.4 6.1 - - - +
49A ALA* 3.9 7.9 - - + -
56A LEU* 4.0 10.0 - - + +
57A ARG* 1.3 73.5 - - - +
59A ILE* 1.3 61.8 + - - +
60A LEU* 4.2 4.9 + - + -
73A LEU 3.7 0.9 - - - +
74A ALA* 3.3 5.4 - - - +
75A LEU* 2.7 43.3 + - + +
77A PHE* 3.8 20.0 - - + -
85A PHE* 4.3 7.9 - - + -
101A PHE* 3.6 38.8 - - + -
112A LEU* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG 3.5 2.1 - - - +
47A ILE* 3.4 6.8 - - - -
48A SER* 2.8 38.6 + - - +
50A SER* 6.1 0.4 - - - +
57A ARG* 4.4 21.3 - - + +
58A LEU* 1.3 76.9 - - - +
60A LEU* 1.3 65.0 + - - +
61A SER* 3.6 17.7 + - - +
72A PRO* 4.6 9.9 - - + -
73A LEU 3.4 9.0 - - - +
74A ALA* 4.9 6.1 - - + -
143B GLN* 3.7 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.2 5.4 - - + -
38A VAL* 4.8 0.4 - - + -
40A PHE* 3.7 44.9 - - + -
45A TYR* 4.0 6.5 - - + -
46A ARG 3.6 2.9 - - - -
47A ILE* 3.5 26.9 - - + -
58A LEU* 4.3 11.7 - - + -
59A ILE* 1.3 75.2 - - - +
61A SER* 1.3 60.6 + - - +
62A PRO* 3.4 4.9 - - - +
72A PRO* 3.3 6.8 - - - +
73A LEU* 2.8 41.3 + - + +
75A LEU* 3.8 21.8 - - + -
101A PHE* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.6 5.5 - - - +
46A ARG* 2.8 40.5 + - - +
48A SER* 5.4 1.4 + - - -
59A ILE* 3.6 19.1 + - - +
60A LEU* 1.3 74.4 + - - +
62A PRO* 1.3 70.7 - - - +
63A LEU* 3.4 2.9 + - - +
72A PRO* 4.3 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 4.0 10.8 - - + -
42A SER* 3.9 10.3 - - - +
44A ALA 3.3 9.4 - - - +
45A TYR* 3.6 3.8 - - + -
60A LEU 3.4 11.4 - - - +
61A SER* 1.3 86.1 - - - +
63A LEU* 1.3 69.3 + - - +
64A PRO* 4.6 0.5 - - - +
66A ALA* 4.3 4.5 - - + -
70A GLN* 3.4 40.4 - - + +
72A PRO* 4.0 16.7 - - + +
----------------------------------------------------------
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