Contacts of the strand formed by residues 106 - 117 (chain A) in PDB entry 3MOK
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 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 3.4 22.2 - - - +
55A GLN* 3.5 4.0 - - - -
100A GLY* 3.5 7.6 - - - -
101A GLY 2.9 29.5 + - - -
102A ALA 4.6 2.6 + - - -
104A SER 3.7 2.3 - - - +
105A GLY* 1.3 82.5 - - - +
107A TYR* 1.3 64.9 + - - -
108A ALA* 3.9 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN* 3.5 24.5 + - - -
44A GLY* 3.3 28.3 + - - -
45A GLY* 3.5 21.7 + - - -
46A PHE 4.3 5.0 + - - -
47A ASN* 4.0 19.5 - - + -
55A GLN* 2.8 39.1 + - + +
57A ALA* 3.6 26.9 - - + -
68A ILE* 3.7 11.8 - - + +
98A LEU* 4.7 4.7 - - + -
99A THR 3.4 12.8 - - - -
100A GLY 3.7 4.9 - - - -
101A GLY* 3.7 18.7 - - - -
102A ALA 4.7 2.2 + - - -
105A GLY 5.1 0.7 - - - +
106A GLY* 1.3 74.3 - - - -
108A ALA* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.6 9.4 - - - -
98A LEU* 3.4 8.3 - - - +
99A THR* 2.8 43.3 + - - +
106A GLY 3.9 2.0 + - - +
107A TYR* 1.3 75.8 - - - +
109A LEU* 1.3 65.6 + - - +
112A GLN* 6.2 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
66A ALA* 3.7 34.3 - - + +
67A PHE 4.3 0.7 - - - +
68A ILE* 3.8 11.5 - - + +
93A ALA* 3.7 29.4 - - + +
94A LEU 3.7 26.9 - - - +
95A GLY* 3.8 5.2 - - - +
96A ASP 4.1 4.0 - - - +
97A THR 3.3 11.9 - - - +
98A LEU* 3.9 8.7 - - + -
99A THR* 4.9 1.8 - - - -
108A ALA* 1.3 77.5 - - - +
110A ASP* 1.3 65.2 + - - +
111A SER 3.9 13.2 - - - +
112A GLN* 4.0 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASP 3.6 9.0 - - - +
97A THR* 2.8 30.1 + - + +
99A THR* 4.2 17.3 - - + +
108A ALA 4.1 0.8 + - - -
109A LEU* 1.3 73.7 - - - +
111A SER* 1.3 62.1 + - - +
112A GLN 4.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY* 3.2 5.5 - - - -
96A ASP* 2.9 43.9 + - - -
109A LEU* 3.9 3.3 - - - +
110A ASP* 1.3 81.8 - - - +
112A GLN* 1.3 59.7 + - - +
113A GLU* 3.6 13.0 + - - +
183A ALA 5.7 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 4.9 6.8 - - - -
8A SER* 4.3 9.5 - - - -
68A ILE* 5.8 1.2 - - - +
93A ALA* 3.8 25.2 - - + +
94A LEU 4.0 4.9 - - - +
109A LEU* 4.0 29.0 + - + +
110A ASP 4.0 2.0 + - - -
111A SER* 1.3 73.5 + - - +
113A GLU* 1.3 63.4 + - - +
114A VAL* 4.4 7.6 - - - +
115A SER* 3.5 19.2 + - - -
181A THR* 4.8 5.4 + - - +
182A PRO 5.3 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.5 0.5 - - - -
8A SER* 2.8 33.8 + - - -
11A TYR* 3.6 27.7 + - + +
19A TYR* 2.7 32.7 + - + +
23A TRP* 4.0 2.9 - - - -
33A ARG* 2.8 41.4 + - - -
94A LEU 2.9 7.4 + - - +
95A GLY* 3.7 13.4 - - - -
96A ASP* 3.8 17.7 - - - +
111A SER* 4.1 11.7 + - - +
112A GLN* 1.3 74.6 - - - +
114A VAL* 1.3 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.1 1.1 - - + -
6A SER 3.3 11.4 - - - +
7A TYR* 4.2 7.9 - - + -
11A TYR* 4.4 5.2 - - + -
19A TYR* 3.7 36.8 - - + -
92A ILE 4.2 0.7 - - - +
93A ALA* 3.6 0.9 - - - +
94A LEU* 2.8 34.1 + - - +
112A GLN* 4.6 4.0 - - - -
113A GLU* 1.3 88.0 - - - +
115A SER* 1.3 62.0 + - - +
116A PHE* 3.5 32.9 - - + -
169A PHE* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.2 9.7 - - - +
6A SER* 2.8 42.4 + - - +
91A SER* 4.8 2.9 - - - -
92A ILE 3.4 9.7 + - - -
93A ALA* 4.1 7.9 - - - +
112A GLN* 3.5 25.3 + - - -
114A VAL* 1.3 73.3 - - - +
116A PHE* 1.3 63.7 + - - +
117A SER* 3.4 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.5 2.2 - - + -
4A SER 3.6 4.0 - - - -
5A ILE* 3.8 29.4 - - + -
16A VAL* 4.0 21.5 - - + -
19A TYR* 5.0 0.9 - + - -
20A LEU* 4.1 7.9 - - + -
91A SER* 3.1 3.6 - - - -
92A ILE* 2.8 47.6 + - + +
94A LEU* 4.0 23.1 - - + -
114A VAL* 3.5 28.7 - - + -
115A SER* 1.3 72.8 + - - +
117A SER* 1.3 61.1 + - - +
119A LEU* 3.7 22.6 - - + +
148A LEU* 4.5 8.7 - - + -
152A ILE* 3.4 37.7 - - + -
169A PHE* 4.7 2.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.5 6.1 - - - +
4A SER* 2.8 40.1 + - - +
90A ASP 3.5 5.8 - - - -
91A SER* 3.9 10.9 - - - -
115A SER* 3.4 19.4 + - - -
116A PHE* 1.3 72.6 + - - +
118A ASN* 1.3 74.6 + - - +
119A LEU 3.2 2.4 + - - -
----------------------------------------------------------
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