Contacts of the strand formed by residues 52 - 61 (chain A) in PDB entry 3O5F
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 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY 3.6 4.0 + - - +
51A ASP* 1.3 73.1 - - - +
53A VAL* 1.3 58.9 + - - +
54A TYR* 3.9 20.8 - - + +
78A VAL* 3.8 22.6 + - - +
79A PHE* 3.5 21.7 - - - +
80A SER* 3.8 19.0 - - - +
85A GLN* 4.8 3.4 + - - +
137A PHE* 3.1 6.8 - - - +
138A LYS* 2.7 42.7 + - + +
139A GLY 5.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.8 24.2 - - + -
51A ASP 4.1 7.4 - - - +
52A LYS* 1.3 76.2 - - - +
54A TYR* 1.3 62.7 + - - +
55A VAL* 4.1 1.1 - - + -
77A PHE 3.6 1.4 - - - +
78A VAL* 3.3 6.9 - - - +
79A PHE* 2.7 82.7 + - + +
81A LEU* 4.3 8.1 - - + +
94A VAL* 4.2 7.9 - - + -
134A LEU* 4.1 10.8 - - + -
136A ASP 3.7 2.5 - - - -
137A PHE* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 3.9 28.0 - - + +
53A VAL* 1.3 76.1 - - - +
55A VAL* 1.3 64.2 + - - +
76A PRO* 4.8 6.7 - - + -
77A PHE 3.5 3.8 - - - -
78A VAL* 3.5 34.6 - - + +
134A LEU* 3.8 0.5 - - - +
135A LEU* 2.8 37.8 + - + +
136A ASP* 3.0 37.8 + - + +
138A LYS* 4.5 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 4.8 0.2 - - + -
54A TYR* 1.3 81.5 - - - +
56A HIS* 1.3 62.7 + - - +
57A TYR* 4.4 3.4 - - + -
70A SER* 4.2 0.3 + - - -
76A PRO* 3.4 5.7 - - - +
77A PHE* 2.8 57.7 + - + +
79A PHE* 4.4 15.0 - - + -
90A TRP* 3.9 31.6 - - + -
94A VAL* 4.5 8.3 - - + -
132A ILE* 4.0 19.5 - - + -
133A GLU 3.2 12.8 - - - +
134A LEU* 4.0 16.6 - - + -
135A LEU* 3.8 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 1.3 74.9 + - - +
57A TYR* 1.3 62.6 + - - +
70A SER* 2.8 29.6 + - - -
71A HIS* 3.5 23.9 - + + +
74A ASN* 3.2 38.3 + - - -
75A GLU 4.0 1.1 - - - -
76A PRO* 3.9 26.8 - - - +
131A GLU 4.0 0.2 - - - +
132A ILE* 3.5 1.7 - - - +
133A GLU* 2.8 49.9 + - + +
135A LEU* 3.8 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.4 0.9 - - + -
56A HIS* 1.3 77.0 - - - +
58A LYS* 1.3 73.1 - - - +
67A PHE* 5.5 0.4 - + - -
68A ASP* 2.7 37.5 + - + -
69A SER* 3.1 17.0 + - - -
70A SER* 2.9 56.7 + - - -
71A HIS* 3.6 4.9 + - - -
77A PHE* 3.9 32.4 - + + -
90A TRP* 3.5 39.5 - + + -
130A PHE* 4.1 10.3 - + + -
131A GLU 3.1 12.1 - - - +
132A ILE* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 1.3 81.9 - - - +
59A GLY* 1.3 58.5 + - - +
60A LYS* 4.3 2.2 - - + -
68A ASP 3.8 5.2 - - - -
69A SER* 3.8 9.0 - - - +
71A HIS* 3.8 26.0 - - + +
129A PHE* 3.9 1.4 - - - +
130A PHE* 3.3 5.0 - - - +
131A GLU* 2.9 60.4 + - + +
141A CO3 3.7 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 4.2 1.8 - - - -
58A LYS* 1.3 73.2 - - - +
60A LYS* 1.3 63.8 + - - +
66A LYS* 3.5 4.5 - - - -
67A PHE* 2.9 46.5 + - - -
68A ASP 2.9 18.8 + - - +
129A PHE 3.4 6.1 - - - -
130A PHE* 3.8 8.3 - - - -
141A CO3 3.8 0.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
58A LYS* 5.2 2.2 - - + -
59A GLY* 1.3 79.7 - - - +
61A LEU* 1.3 66.2 + - - +
64A GLY* 3.4 32.4 + - - +
65A LYS 3.2 8.7 - - - +
66A LYS* 4.1 4.5 - - - +
67A PHE* 3.3 9.7 - - - -
128A LEU 3.8 0.2 - - - -
129A PHE* 2.8 61.0 + - + +
141A CO3 3.3 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 4.6 3.3 + - - -
60A LYS* 1.3 76.9 - - - +
62A SER* 1.3 61.4 + - - +
63A ASN* 3.2 26.0 - - - +
64A GLY* 2.8 20.7 + - - -
65A LYS* 2.8 29.7 + - + +
66A LYS 5.7 0.2 - - - +
67A PHE* 3.6 21.1 - - + -
121A LYS 3.9 18.4 - - - +
122A ILE* 4.5 2.5 - - + -
123A PRO* 3.9 29.6 - - + -
126A ALA* 4.5 4.7 - - + -
127A THR 4.1 4.5 - - - +
128A LEU* 3.7 17.9 - - + -
129A PHE* 4.8 2.2 - - - +
----------------------------------------------------------
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