Contacts of the strand formed by residues 51 - 58 (chain B) in PDB entry 1MKG
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 CYS 51 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A SER* 2.9 34.7 + - - -
59A GLY* 3.6 9.2 - - - -
60A CYS* 2.1 56.9 - - + -
32B LEU* 4.6 5.6 - - - -
33B VAL 3.0 20.9 - - - +
34B ASP* 3.9 5.2 - - + +
35B ILE 4.0 1.6 - - - +
49B PRO* 3.3 10.1 - - - +
50B SER* 1.3 79.8 - - - +
52B VAL* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.2 6.1 - - + -
32B LEU* 4.4 2.9 - - - -
33B VAL* 2.7 40.4 + - + +
35B ILE* 3.8 6.1 - - + +
49B PRO* 5.2 0.4 - - + -
51B CYS* 1.3 78.4 - - - +
53B PRO* 1.4 69.1 - - + +
54B LEU* 3.3 22.6 + - + -
78B MET* 3.8 14.1 - - - -
80B ILE* 3.5 31.9 - - + -
96B PHE* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.0 18.6 - - + +
23A ARG* 3.9 36.9 + - + +
24A SER* 4.1 8.5 - - - -
30B GLU* 4.0 27.1 - - - +
31B THR 3.5 6.7 - - - +
32B LEU* 3.7 20.3 - - + -
52B VAL* 1.4 84.5 - - + +
54B LEU* 1.3 58.5 + - - +
78B MET* 3.6 20.9 - - + +
98B GLN* 4.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 4.4 1.8 - - - -
31B THR* 2.6 46.9 + - - +
33B VAL* 3.8 19.3 - - + -
38B GLU* 4.6 0.4 - - + -
52B VAL* 3.8 20.4 - - + +
53B PRO* 1.3 80.2 - - - +
55B MET* 1.3 62.3 + - - +
56B ARG* 3.3 33.4 + - - +
76B ILE* 3.8 18.6 - - + -
78B MET* 4.6 3.4 - - + -
96B PHE* 3.4 36.3 - - + -
97B LEU 3.7 8.3 - - - +
98B GLN* 4.0 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO* 4.6 10.1 - - + +
29B ILE* 3.7 7.2 - - - -
30B GLU* 3.3 52.5 - - + +
54B LEU* 1.3 69.4 - - - +
56B ARG* 1.3 64.7 + - - +
98B GLN* 3.2 26.3 - - - +
99B HIS 2.9 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO* 3.9 2.2 - - - -
29B ILE* 2.8 39.4 + - - +
31B THR* 3.8 19.9 + - + +
33B VAL* 4.4 7.2 - - + +
37B GLN* 4.0 19.2 - - - +
38B GLU* 2.9 33.3 + - - -
54B LEU* 3.3 24.1 + - + +
55B MET* 1.3 80.8 + - - +
57B ALA* 1.3 69.9 + - - +
58B GLY 3.2 0.7 + - - -
97B LEU* 2.8 38.9 + - - +
99B HIS* 3.4 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS 3.8 5.2 - - - -
28B PRO* 4.2 0.4 - - - -
56B ARG* 1.3 73.4 - - - +
58B GLY* 1.3 58.3 + - - +
68B CYS* 4.2 12.8 - - - +
69B VAL* 4.2 1.8 - - - -
70B PRO* 3.9 21.1 - - + -
99B HIS* 2.9 23.2 + - + +
102B ALA* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.6 13.9 - - - -
26B CYS* 3.1 6.4 - - - -
27B HIS 2.8 33.7 + - - -
29B ILE* 4.6 4.0 - - - -
56B ARG 3.2 3.0 + - - -
57B ALA* 1.3 74.8 - - - +
59B GLY* 1.3 62.8 + - - -
68B CYS* 3.1 5.2 - - - -
----------------------------------------------------------
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