Contacts of the strand formed by residues 74 - 81 (chain A) in PDB entry 5MLG
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 GLN 74 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 3.5 1.1 - - - -
69A ILE 2.9 35.3 + - - +
72A PRO 4.1 7.3 + - - +
73A SER* 1.3 73.1 - - - +
75A THR* 1.3 60.5 + - - +
76A PHE* 3.3 20.7 - - + -
106A LEU 3.5 10.9 - - - +
107A TYR* 3.6 16.8 - - - -
108A ASP* 2.8 48.0 + - - +
111A GLU* 3.9 30.7 - - + +
112A SER* 4.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 3.9 34.5 - - + +
67A ILE 3.4 11.2 - - - +
68A GLY* 4.6 1.5 - - - -
73A SER* 3.9 5.2 + - - -
74A GLN* 1.3 72.6 - - - +
76A PHE* 1.3 71.4 + - - +
77A LYS* 5.9 1.1 - - + -
105A ASN* 3.7 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY 3.8 0.2 - - - +
66A GLU* 3.3 6.5 - - - +
67A ILE* 3.0 36.8 + - + +
69A ILE* 3.9 29.4 - - + -
74A GLN* 3.3 33.2 - - + -
75A THR* 1.3 76.7 - - - +
77A LYS* 1.3 62.4 + - - +
78A VAL* 3.8 8.6 + - + -
89A VAL* 3.8 30.5 - - + -
105A ASN* 3.5 37.5 - - + +
106A LEU 3.7 2.9 - - - -
107A TYR* 3.4 37.9 - + + -
168A ASP* 3.5 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.5 49.5 + - + -
65A GLY 3.5 5.2 - - - -
66A GLU* 4.0 15.0 - - + +
75A THR* 5.9 0.7 - - + -
76A PHE* 1.3 73.5 - - - +
78A VAL* 1.3 59.5 + - - +
105A ASN* 4.9 7.6 - - - +
166A LYS 4.0 14.9 + - - +
167A PHE* 3.7 5.1 - - - -
168A ASP* 2.8 50.7 + - - +
169A GLY 3.1 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.2 6.3 - - - +
65A GLY 2.8 41.5 + - - +
67A ILE* 3.8 46.7 - - + -
76A PHE* 4.3 9.0 - - + -
77A LYS* 1.3 78.4 - - - +
79A ILE* 1.3 62.2 + - - +
80A PHE* 3.9 8.7 + - + -
87A LEU* 4.7 1.1 - - + -
89A VAL* 4.4 5.8 - - + -
167A PHE* 4.9 0.2 - - - -
169A GLY* 3.2 23.3 - - - +
170A VAL 4.1 4.3 - - - +
171A LEU* 4.0 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET* 4.3 2.0 - - + -
58A TYR* 3.7 21.1 - - + -
61A THR* 3.6 32.5 - - + -
63A TYR 3.9 11.4 - - - +
78A VAL* 1.3 72.5 - - - +
80A PHE* 1.3 73.3 + - - +
81A ASP* 3.3 13.7 + - + -
167A PHE* 3.4 53.6 - - + -
169A GLY 3.1 8.2 + - - +
170A VAL* 3.7 6.3 - - + +
171A LEU 2.9 26.7 + - - +
267A THR 5.0 0.9 - - - +
268A GLY* 4.3 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.6 50.0 - - + -
13A LEU* 4.0 19.9 - - + +
63A TYR 5.1 2.0 + - - -
65A GLY* 3.9 13.4 - - - +
67A ILE* 4.4 3.4 - - + -
78A VAL* 4.0 16.2 - - + -
79A ILE* 1.3 74.5 - - - +
81A ASP* 1.3 53.7 + - - +
82A THR 4.0 0.2 - - - -
142A VAL* 4.1 7.2 - - + -
171A LEU* 3.6 30.1 - - + -
173A MET* 4.0 28.3 - - + -
203A VAL* 6.4 1.3 - - + -
205A TYR* 4.8 1.3 + - - +
216A VAL* 4.4 23.3 - - + -
267A THR* 2.6 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 4.3 7.2 - - - +
58A TYR* 2.9 25.0 + - - +
79A ILE* 4.1 6.3 - - + -
80A PHE* 1.3 71.0 - - - +
82A THR* 1.3 59.1 + - - +
83A GLY* 3.0 10.0 + - - -
84A SER* 3.1 34.8 + - - +
170A VAL* 3.8 19.3 - - + -
171A LEU 3.1 7.5 + - - +
172A GLY* 3.5 1.2 - - - -
173A MET* 3.0 20.4 + - - +
266A ASP* 3.0 23.7 - - - +
267A THR* 3.6 1.3 - - - -
268A GLY* 3.4 14.6 - - - +
----------------------------------------------------------
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