Contacts of the strand formed by residues 103 - 110 (chain A) in PDB entry 5MJ0
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 103 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 4.0 9.0 - - - -
52A LEU 5.7 0.7 - - - -
101A ASN 3.5 1.4 + - - -
102A SER* 1.3 75.3 - - - +
104A THR* 1.3 62.5 + - - -
105A TYR* 3.6 9.2 - - - -
123A ILE* 3.7 3.7 - - - +
124A LEU 2.8 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 5.2 1.8 - - + -
51A LYS* 3.7 5.1 - - - +
52A LEU* 2.8 58.5 + - + +
103A GLY* 1.3 72.6 - - - -
105A TYR* 1.3 68.2 + - - +
121A LYS* 4.6 15.3 - - + -
122A VAL 3.6 13.0 - - - +
123A ILE* 3.8 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.5 30.1 - - + -
49A TRP* 4.1 5.4 - + + -
50A VAL 3.4 16.4 - - - +
51A LYS* 3.7 20.9 - - + +
52A LEU* 3.4 3.7 - - - +
92A LEU* 4.7 4.0 - - + -
94A ILE* 4.2 17.0 - - + +
101A ASN* 2.7 36.8 + - - +
103A GLY 3.6 17.9 - - - -
104A THR* 1.3 76.9 - - - +
106A ARG* 1.3 61.2 + - - +
121A LYS* 3.3 6.6 - - - +
122A VAL* 2.8 41.9 + - + +
124A LEU* 3.9 16.7 - - + +
53B LEU* 3.4 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 3.9 1.7 + - - +
49A TRP* 3.6 5.1 - - - -
50A VAL* 3.1 59.9 + - + +
52A LEU* 3.5 25.6 - - + +
105A TYR* 1.3 73.7 - - - +
107A CYS* 1.3 64.6 + - - +
108A THR* 2.3 35.3 + - - +
119A SER* 3.5 19.5 + - - -
120A GLY 3.4 13.2 - - - +
121A LYS* 4.2 17.3 - - + +
50B VAL* 5.5 5.5 - - - +
106B ARG* 5.2 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 2.0 55.0 - - - -
36A THR 3.5 8.3 - - - -
37A ALA* 3.8 7.2 - - - -
47A VAL* 4.5 3.1 - - + -
48A SER 3.3 7.0 - - - +
49A TRP* 3.6 29.3 - - + +
106A ARG* 1.3 73.5 - - - +
108A THR* 1.3 62.1 + - - +
118A LEU 3.8 0.2 - - - +
119A SER* 3.2 6.1 - - - -
120A GLY 3.0 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR 3.5 3.5 - - - +
47A VAL* 3.6 0.3 - - - -
48A SER* 3.0 47.1 + - - +
106A ARG* 2.3 42.1 + - - +
107A CYS* 1.3 72.8 + - - +
109A LEU* 1.3 66.2 + - - +
110A GLN* 3.9 2.4 + - + +
117A ASN* 3.8 31.0 - - + +
118A LEU 3.2 9.6 - - - +
119A SER* 3.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 4.2 7.9 - - - -
37A ALA* 4.1 10.5 - - + -
39A TRP* 3.7 37.2 - - + -
45A TYR* 3.5 30.3 - - + -
46A THR 3.2 12.6 - - - +
47A VAL* 3.7 26.7 - - + -
90A TYR* 3.8 30.1 - - + -
108A THR* 1.3 73.6 - - - +
110A GLN* 1.3 57.6 + - - +
117A ASN* 3.1 8.1 - - - -
118A LEU* 2.7 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.6 4.2 - - - -
46A THR* 3.0 45.3 + - - +
108A THR* 3.9 2.9 + - + +
109A LEU* 1.3 71.5 - - - +
111A ASP* 1.3 81.3 + - - +
112A PRO* 3.4 5.8 - - + +
114A GLY 3.6 4.8 + - - -
115A GLN* 4.2 3.8 - - - +
116A ARG 2.7 34.8 + - - +
117A ASN* 3.7 17.3 + - + +
----------------------------------------------------------
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