Contacts of the strand formed by residues 51 - 57 (chain B) in PDB entry 5C1Q
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 SER 51 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.3 15.7 - - - -
45B GLY 3.2 9.0 - - - -
46B SER* 4.8 6.2 + - - -
49B PHE* 4.5 0.2 - - - -
50B GLY* 1.3 76.5 + - - -
52B VAL* 1.3 66.2 + - - +
53B TYR* 4.3 12.3 - - - -
66B ILE 3.5 2.8 - - - +
67B LYS* 3.5 0.3 - - - -
68B HIS* 2.9 39.4 + - - +
73B ARG* 5.8 0.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
43B LEU* 3.6 2.4 - - - +
44B LEU* 2.7 37.4 + - + -
45B GLY* 2.7 20.3 + - - +
49B PHE* 3.9 24.5 - - + -
51B SER* 1.3 79.0 - - - +
53B TYR* 1.3 59.0 + - - +
65B ALA* 4.3 19.1 - - + -
66B ILE 3.4 9.2 - - - +
67B LYS* 4.1 20.4 - - + -
120B LEU* 5.8 0.2 - - + -
401B 4YK 4.2 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.2 16.6 - - + -
41B GLY 3.9 10.8 - - - +
42B PRO 3.3 9.0 - - - +
43B LEU* 3.3 47.4 - - + +
44B LEU* 4.1 4.0 - - - -
51B SER* 4.4 11.5 - - - -
52B VAL* 1.3 73.9 - - - +
54B SER* 1.3 68.8 + - - +
65B ALA* 3.4 4.7 - - - +
66B ILE* 2.7 44.5 + - + +
68B HIS* 3.6 36.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.3 0.7 - - - -
41B GLY* 2.9 24.8 + - - -
42B PRO* 3.0 25.3 + - - +
44B LEU* 3.6 28.8 - - - +
53B TYR* 1.3 76.6 - - - +
55B GLY* 1.3 57.3 + - - +
64B VAL 4.0 5.6 - - - -
66B ILE* 4.8 0.2 - - - -
122B ARG* 3.1 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN 3.4 11.7 - - - -
41B GLY* 4.2 1.1 - - - -
54B SER* 1.3 77.4 + - - +
56B ILE* 1.3 62.6 + - - -
64B VAL* 2.8 33.3 + - - -
66B ILE* 4.0 10.8 - - - -
122B ARG* 2.7 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 3.3 4.7 - - - -
39B GLN* 3.0 51.4 + - + +
41B GLY* 5.7 2.0 - - - +
55B GLY* 1.3 78.8 - - - +
57B ARG* 1.3 65.4 + - - +
58B VAL* 3.4 1.3 + - - -
61B ASN* 3.7 35.7 - - + +
62B LEU 3.5 4.0 - - - +
63B PRO* 5.0 1.8 - - + -
64B VAL* 3.8 3.3 - - - +
122B ARG* 4.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN* 3.4 27.4 - - - +
38B TYR* 3.5 33.3 + - + -
56B ILE* 1.3 70.5 - - - +
58B VAL* 1.3 55.5 + - - +
59B SER* 3.5 12.3 + - - +
60B ASP* 3.0 31.6 + - - +
61B ASN* 2.6 36.4 + - - -
62B LEU* 2.8 53.7 + - + +
64B VAL* 4.4 5.0 - - + +
107B LEU* 5.0 17.4 - - - +
----------------------------------------------------------
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