Contacts of the strand formed by residues 51 - 56 (chain A) in PDB entry 5Z7R
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 ALA 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS 3.4 3.4 + - - -
14A VAL* 3.5 4.8 - - + -
15A ALA 2.9 24.2 + - - -
49A VAL* 3.4 7.8 - - - +
50A LEU* 1.3 82.4 - - - +
52A VAL* 1.3 66.3 + - - +
98A LYS* 4.2 2.0 - - - -
99A PRO* 3.5 13.7 - - + +
101A ILE* 5.3 2.2 - - + -
196A ALA* 4.4 21.5 - - + +
199A ILE* 4.6 9.4 - - + -
200A VAL* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 3.2 9.9 - - - +
17A VAL* 4.1 17.0 - - + -
43A ILE* 3.8 36.8 - - + -
49A VAL* 4.2 2.0 - - + -
51A ALA* 1.3 81.5 - - - +
53A ILE* 1.3 79.1 + - - +
54A LEU* 4.5 2.2 - - + +
93A LEU* 5.5 4.7 - - + -
96A LEU* 4.3 12.6 - - + -
98A LYS* 4.8 3.1 - - + -
99A PRO 2.9 7.8 + - - +
100A VAL* 3.3 23.5 - - + -
101A ILE* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.1 20.6 - - + -
15A ALA 2.9 8.2 + - - +
16A VAL* 3.4 10.7 - - + +
17A VAL* 2.7 30.5 + - - +
52A VAL* 1.3 80.9 - - - +
54A LEU* 1.3 68.6 + - - +
55A THR 4.9 0.2 - - - +
101A ILE* 3.2 12.6 - - + +
103A ALA* 4.1 8.1 - - + -
189A MET* 4.0 19.7 - - + -
192A ALA* 3.9 38.6 - - + +
193A LYS* 3.9 24.5 - - + -
196A ALA* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.3 30.1 - - + +
19A ILE* 4.2 16.2 - - + -
36A MET* 4.7 7.0 - - - -
52A VAL* 4.2 2.4 - - + -
53A ILE* 1.3 75.1 - - - +
55A THR* 1.3 68.4 + - - +
62A PHE* 3.9 21.2 - - + -
93A LEU* 4.4 7.6 - - + -
100A VAL* 4.8 5.2 - - + -
101A ILE 2.7 10.7 + - - +
102A ALA* 3.5 4.9 - - - -
103A ALA 2.8 26.2 + - - +
115A ILE* 3.9 27.4 - - + -
119A CYS* 3.8 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.7 5.6 - - + -
17A VAL 2.9 8.6 + - - +
18A THR* 3.1 21.9 - - + +
19A ILE* 2.9 25.5 + - - +
53A ILE* 5.0 0.4 - - - -
54A LEU* 1.3 81.6 - - - +
56A GLY* 1.3 67.6 + - - +
62A PHE* 3.8 8.3 - - - -
103A ALA* 2.7 31.2 + - - +
105A ASN* 2.7 21.0 + - - +
188A LEU* 5.2 0.2 - - - +
189A MET* 4.3 18.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.5 5.4 - - - +
19A ILE* 3.4 10.5 - - - -
55A THR* 1.3 95.9 + - - +
57A ALA* 1.3 60.2 + - - -
58A GLY 4.6 0.9 - - - +
61A SER 3.9 1.1 - - - -
62A PHE* 3.4 25.9 - - - -
105A ASN* 3.0 17.7 + - - +
----------------------------------------------------------
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