Contacts of the strand formed by residues 136 - 142 (chain B) in PDB entry 3VKO
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 ASP 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.5 13.1 - - + +
23B ILE* 2.8 33.7 + - - +
25B ASP 6.0 0.4 - - - -
51B GLN 3.0 1.4 + - - -
52B ASN* 4.5 3.6 - - - +
53B GLY* 2.7 35.8 + - - -
134B LYS 4.5 4.5 - - - +
135B ILE* 1.3 76.3 - - - +
137B THR* 1.3 79.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.8 27.4 - - + -
21B GLY 3.3 14.5 + - - +
22B THR* 4.7 4.9 + - - -
23B ILE* 3.9 8.9 - - - +
49B ASP 3.7 0.2 - - - +
50B LEU* 3.6 4.7 - - - -
51B GLN* 2.7 39.3 + - - +
53B GLY* 3.6 25.9 - - - +
54B SER* 4.1 5.5 + - - -
135B ILE 3.9 0.2 - - - -
136B ASP* 1.3 102.6 + - - +
138B LEU* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 3.5 11.7 - - + +
20B VAL* 3.4 3.3 - - - -
21B GLY 2.8 35.9 + - - +
23B ILE* 4.0 14.5 - - + +
33B ILE* 4.7 6.7 - - + -
35B ILE* 4.5 9.0 - - + -
48B VAL* 4.0 17.7 - - + -
49B ASP 3.6 2.7 - - - +
50B LEU* 3.8 24.7 - - + -
137B THR* 1.3 74.7 - - - +
139B GLY* 1.3 63.8 + - - +
140B ILE* 4.3 9.9 - - + -
149B ILE* 3.8 43.1 - - + -
151B PHE* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE 3.2 6.1 - - - -
20B VAL* 4.5 2.0 - - - -
47B GLN 3.7 0.3 - - - +
48B VAL* 3.4 0.3 - - - -
49B ASP 2.7 42.9 + - - +
51B GLN* 3.9 5.4 + - - -
137B THR 4.1 0.8 - - - -
138B LEU* 1.3 75.0 - - - +
140B ILE* 1.3 66.6 + - - +
141B TYR* 3.7 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 4.2 5.5 - - + +
18B PRO* 3.4 4.0 - - - +
19B PHE* 2.8 47.1 + - + +
35B ILE* 4.1 20.4 - - + -
46B PHE* 5.3 0.7 - - + -
47B GLN 3.3 8.5 - - - +
48B VAL* 4.3 13.7 - - + -
138B LEU* 4.3 11.0 - - + -
139B GLY* 1.3 79.2 - - - +
141B TYR* 1.3 63.2 + - - +
144B VAL* 4.0 17.0 - - + -
146B ILE* 4.0 34.1 - - + -
149B ILE* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 4.8 1.6 - - - -
18B PRO* 3.7 25.1 - - + -
19B PHE 4.3 1.3 - - - -
20B VAL* 3.5 30.4 - - + +
46B PHE* 3.2 6.9 - - - +
47B GLN* 2.9 51.6 + - + +
49B ASP* 3.4 25.8 - - - -
51B GLN* 2.6 28.9 + - - -
56B MET* 5.0 14.9 - - + +
59B ARG* 5.8 1.8 - - - -
139B GLY* 3.7 17.2 - - - -
140B ILE* 1.3 76.0 - - - +
142B GLY* 1.3 62.4 + - - +
144B VAL* 4.4 2.8 - - - +
3D SIA 6.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 3.8 15.7 - - - +
18B PRO* 5.4 1.2 - - - +
45B ARG* 3.8 8.7 - - - -
46B PHE* 4.0 1.8 - - - -
47B GLN* 5.9 0.9 - - - -
141B TYR* 1.3 79.5 - - - +
143B LYS* 1.3 63.5 + - - -
144B VAL* 3.2 7.0 + - - +
----------------------------------------------------------
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