Contacts of the strand formed by residues 57 - 66 (chain A) in PDB entry 5UWS
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 GLY 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS* 4.9 0.2 - - - -
54A THR* 2.6 44.2 + - - +
55A ASN 3.4 1.6 + - - -
56A ARG* 1.3 78.3 - - - +
58A PRO* 1.3 76.7 - - - +
59A ILE* 4.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.9 26.6 - - + +
51A VAL* 4.2 16.2 - - + -
52A PHE 3.3 12.1 - - - +
53A HIS* 4.4 14.3 - - + +
57A GLY* 1.3 85.1 - - - +
59A ILE* 1.3 59.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
9A VAL* 4.4 4.3 - - + +
11A PHE* 3.6 37.9 - - + -
50A LEU 3.8 0.7 - - - +
51A VAL* 3.4 4.7 - - - -
52A PHE* 3.0 44.7 + - + +
54A THR* 3.9 18.2 - - + -
57A GLY 4.9 0.4 - - - +
58A PRO* 1.3 74.7 - - - +
60A LYS* 1.3 62.6 + - - +
61A PHE* 3.9 30.3 + - + -
165A ALA* 4.0 23.1 - - + +
168A LEU* 4.7 1.6 - - + -
169A ILE* 4.0 16.6 - - + -
174A LEU* 5.9 0.7 - - + -
176A PHE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.4 10.4 + - + +
10A GLN* 3.2 40.4 + - + +
11A PHE* 2.9 30.7 + - - -
49A PRO* 4.4 13.6 - - - +
50A LEU 3.4 7.6 - - - +
51A VAL* 4.0 22.9 - - + +
58A PRO 4.3 0.2 - - - -
59A ILE* 1.3 73.9 - - - +
61A PHE* 1.3 74.6 + - - +
62A ASN* 4.0 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.4 7.4 - - + -
13A LEU* 3.7 22.7 - - + -
48A HIS 3.5 0.5 - - - +
49A PRO* 3.4 2.4 - - - +
50A LEU* 2.6 43.7 + - + +
52A PHE* 3.9 26.2 - + - -
59A ILE* 3.9 31.0 - - + -
60A LYS* 1.3 74.8 - - - +
62A ASN* 1.3 61.2 + - - +
63A VAL* 3.5 19.8 + - + -
85A CYS* 4.0 12.3 - - - -
161A PHE* 3.9 36.6 - + + -
164A LEU* 4.2 5.2 - - + -
165A ALA* 4.0 8.3 - - + -
168A LEU* 3.6 23.3 - - + -
176A PHE* 6.2 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 2.6 39.9 + - - +
11A PHE 2.8 14.9 + - - +
12A LYS* 3.7 6.7 - - + +
13A LEU 3.0 22.1 + - - +
47A VAL* 4.8 7.8 - - + +
48A HIS 4.0 3.4 - - - -
49A PRO* 4.0 16.9 - - - +
60A LYS* 4.0 13.3 - - - +
61A PHE* 1.3 72.7 - - - +
63A VAL* 1.3 64.0 + - - +
64A TRP* 3.3 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.4 23.6 - - + -
15A LEU* 4.4 5.6 - - + -
27A VAL* 4.0 34.3 - - + -
46A GLU 3.3 6.6 - - - +
47A VAL* 3.3 1.7 - - - -
48A HIS* 3.0 40.7 + - - +
50A LEU* 4.3 13.2 - - + -
61A PHE* 4.0 22.0 - - + +
62A ASN* 1.3 70.1 - - - +
64A TRP* 1.3 62.9 + - - +
65A ASP* 3.4 8.1 + - + +
161A PHE* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 3.5 37.7 - - + +
13A LEU 2.6 14.2 + - - +
14A VAL* 4.1 9.4 - - + -
15A LEU 3.1 23.8 + - - -
45A VAL* 3.8 12.1 - - + -
46A GLU 3.9 3.6 - - - -
47A VAL* 3.7 26.5 - - + +
62A ASN* 3.3 20.8 + - - +
63A VAL* 1.3 72.1 - - - +
65A ASP* 1.3 60.0 + - - +
66A THR* 3.2 10.4 + - + +
79A TYR* 3.5 31.2 - + + -
23C PHE* 3.3 49.1 - + - -
24C TYR* 4.2 17.5 - + - -
31C GLN* 3.5 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.0 18.1 - - + +
23A LYS* 3.7 15.2 - - - +
24A THR* 2.4 47.0 + - - +
27A VAL* 4.5 9.6 - - + +
42A THR* 3.7 7.2 + - - +
45A VAL* 3.2 3.0 - - - -
46A GLU* 2.8 49.7 + - + +
48A HIS* 4.6 6.9 - - + -
63A VAL* 3.4 2.5 + - + -
64A TRP* 1.3 69.2 - - - +
66A THR* 1.3 70.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 5.3 1.6 - - + -
15A LEU 2.8 23.1 + - - +
16A VAL* 3.5 23.0 - - + +
23A LYS* 3.1 22.5 - - - -
42A THR* 4.3 5.6 - - - -
44A GLY 3.5 8.5 - - - -
45A VAL* 3.8 14.1 - - + -
64A TRP* 3.5 15.0 - - + +
65A ASP* 1.3 79.7 - - - +
67A ALA* 1.3 64.1 + - - +
79A TYR* 3.8 27.8 - - + -
80A TYR* 4.6 4.6 + - + -
104A TRP* 5.3 1.6 - - - -
----------------------------------------------------------
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