Contacts of the strand formed by residues 33 - 38 (chain X) in PDB entry 4MXV
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 VAL 33 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X MET* 4.5 14.4 - - + -
23X CYS* 5.2 0.2 - - - -
29X VAL* 4.6 5.2 - - + -
31X SER 2.5 15.4 + - - +
32X ALA* 1.3 79.9 - - - +
34X ALA* 1.3 70.4 + - - +
35X TRP* 4.4 13.2 - - - +
48X ILE* 4.7 0.5 - - - +
49X TYR 3.6 0.7 - - - -
50X SER* 3.3 8.2 + - - +
51X ALA* 2.7 31.8 + - - +
71X PHE* 3.3 58.8 - - + -
88X CYS* 4.6 4.3 - - + -
89X GLN 3.3 14.6 - - - +
91X SER* 4.5 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33X VAL* 1.3 75.4 - - - +
35X TRP* 1.3 67.6 + - - +
36X TYR* 4.0 13.5 - - + +
46X LEU* 4.3 5.8 - - + -
48X ILE 3.0 14.6 - - - +
49X TYR* 4.2 8.1 - - + -
88X CYS* 3.2 4.7 - - - -
89X GLN* 2.8 51.0 + - - +
91X SER* 4.2 6.5 + - - +
100Y TRP* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 35 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X GLN* 4.3 4.9 - - - -
21X ILE* 3.8 30.1 - - + -
22X THR 4.5 0.2 - - - -
23X CYS* 3.5 31.4 - - + -
33X VAL* 4.4 10.2 - - + +
34X ALA* 1.3 78.8 + - - +
36X TYR* 1.3 66.4 + - - +
46X LEU* 3.7 2.8 - - - +
47X LEU* 3.0 27.5 + - + -
48X ILE* 2.8 39.4 + - + +
51X ALA* 4.4 7.5 + - - +
64X GLY* 5.1 0.4 - - - -
65X SER 5.3 0.4 + - - -
71X PHE* 3.9 10.7 - - + +
72X THR 3.7 12.7 + - - -
73X LEU* 3.4 58.8 - - + -
86X TYR* 4.9 1.3 - - + -
87X TYR 3.2 22.4 - - - -
88X CYS* 3.5 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34X ALA* 4.0 12.1 - - + +
35X TRP* 1.3 77.2 - - - +
37X GLN* 1.3 62.0 + - - +
44X PRO* 4.2 22.2 - - + -
45X LYS 3.2 21.8 - - - +
46X LEU* 3.6 17.6 - - + +
47X LEU* 4.1 5.1 - - - +
86X TYR* 3.2 8.1 - - - +
87X TYR* 2.7 48.3 + - + +
89X GLN* 3.4 30.2 + - + -
98X PHE* 3.7 23.1 - + + -
45Y LEU* 5.6 0.2 - - + -
99Y PRO 4.3 0.9 + - - -
100Y PHE* 3.2 58.8 + + + +
103Y TRP* 4.1 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36X TYR* 1.3 74.8 - - - +
38X GLN* 1.3 64.0 + - - +
39X LYS* 3.9 25.1 + - - +
43X ALA 4.3 0.2 - - - +
44X PRO* 3.3 3.3 - - - +
45X LYS* 2.8 56.3 + - + +
47X LEU* 3.8 22.9 - - + +
62X PHE* 4.4 7.9 - - - -
81X GLU 4.1 8.1 + - - -
82X ASP* 4.4 6.3 + - - -
84X ALA* 3.7 14.7 - - + +
85X THR 3.6 2.0 - - - -
86X TYR* 3.4 33.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X GLN* 1.3 76.5 - - - +
39X LYS* 1.3 69.8 + - - +
40X PRO* 4.9 0.7 - - - +
41X GLY 6.0 0.2 - - - +
42X LYS 3.0 26.7 + - - +
43X ALA 3.9 1.6 - - - -
44X PRO* 3.5 32.2 - - + +
84X ALA* 3.8 0.6 - - - -
85X THR* 2.8 45.3 + - - +
87X TYR* 3.3 23.8 + - + -
39Y GLN* 3.1 41.1 + - - +
91Y TYR* 4.0 2.6 + - - -
----------------------------------------------------------
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