Contacts of the strand formed by residues 34 - 39 (chain M) in PDB entry 2ZPK
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 ASN 34 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I PRO 4.3 5.4 - - - +
98I GLY* 4.2 3.1 - - - -
99I PHE* 2.8 53.5 + - - +
32M TYR 3.9 6.5 - - - +
33M ALA* 1.3 74.1 - - - +
35M TRP* 1.3 72.9 + - - +
36M VAL* 4.0 5.9 - - - +
46M GLY* 5.2 1.4 - - - -
48M ILE 2.8 25.4 + - - -
49M VAL* 3.7 12.9 - - - +
87M PHE 3.8 0.2 - - - +
88M CYS* 3.2 6.8 - - - +
89M ALA* 2.8 40.1 + - + +
96M TRP* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 35 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M GLN* 3.6 21.3 - - - -
21M LEU* 3.7 24.0 - - + -
22M THR 3.8 7.4 - - - -
23M CYS* 3.6 32.3 - - + -
33M ALA* 4.6 5.6 - - - +
34M ASN* 1.3 77.0 + - - +
36M VAL* 1.3 63.6 + - - +
47M LEU* 2.8 28.7 + - + -
48M ILE* 2.9 44.0 + - + +
51M THR 4.9 3.4 + - - -
64M GLY* 5.2 0.2 - - - -
65M SER 5.5 0.2 + - - -
71M ALA* 3.9 7.4 - - - +
72M ALA* 3.7 23.2 + - - +
73M LEU* 3.5 50.5 - - + -
86M TYR* 4.6 6.5 - - + -
87M PHE 3.3 18.4 - - - -
88M CYS* 3.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I LEU* 6.5 0.2 - - + -
99I PHE* 3.5 24.5 - - + +
103I TRP* 3.7 24.9 - - + +
34M ASN* 4.0 14.4 - - - +
35M TRP* 1.3 79.3 - - - +
37M GLN* 1.3 65.3 + - - +
38M GLU 4.2 0.2 + - - -
44M PHE* 3.7 29.4 - - + -
45M THR 3.4 13.0 - - - +
46M GLY* 4.3 1.3 - - - -
47M LEU* 4.3 4.3 - - - +
85M ILE 3.9 0.2 - - - +
86M TYR* 3.4 4.7 - - - +
87M PHE* 2.8 44.8 + - + +
89M ALA* 6.1 1.1 - - + +
98M PHE* 5.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M VAL* 1.3 75.9 - - - +
38M GLU* 1.3 62.6 + - - +
39M LYS* 3.4 37.4 + - - +
43M LEU 3.4 1.7 - - - +
44M PHE* 3.2 5.1 - - - -
45M THR* 2.8 52.9 + - - +
47M LEU* 3.8 23.0 - - + +
62M PHE* 4.4 10.3 - - - -
81M GLU 4.4 3.6 + - - -
82M ASP* 4.4 3.4 + - - +
84M ALA* 3.5 17.5 - - + +
85M ILE 3.5 3.1 - - - +
86M TYR* 3.0 30.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I LYS* 4.7 6.8 - - - -
37M GLN* 1.3 74.7 - - - +
39M LYS* 1.3 73.1 + - - +
40M PRO* 4.9 0.3 - - - +
42M HIS* 3.0 35.2 + - - -
43M LEU 3.4 4.7 - - - +
44M PHE* 3.4 35.9 - - + -
84M ALA* 3.4 4.2 - - - +
85M ILE* 2.7 54.8 + - + +
87M PHE* 3.3 25.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M GLN* 3.4 31.3 + - - +
38M GLU* 1.3 80.5 - - - +
40M PRO* 1.4 74.7 - - + +
42M HIS* 3.3 3.3 + - - -
43M LEU* 2.7 44.1 + - + +
81M GLU* 2.9 49.6 + - - +
82M ASP* 5.5 0.2 + - - -
83M GLU 4.4 7.6 - - - +
84M ALA* 3.8 11.9 - - + -
167M LYS* 5.9 4.0 - - - +
----------------------------------------------------------
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