Contacts of the strand formed by residues 46 - 55 (chain B) in PDB entry 6D6Q
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 LYS 46 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.0 30.7 - - + +
40B ILE 3.4 6.5 - - - -
41B GLU* 3.8 17.0 + - + -
43B GLY 5.1 0.6 + - - -
44B ASN* 3.3 13.4 + - - +
45B THR* 1.3 89.5 - - - +
47B ALA* 1.3 62.9 + - - +
126B VAL* 3.8 1.0 - - - -
127B LEU* 2.9 44.2 + - + +
128B GLN* 2.6 40.0 + - + +
41E VAL* 4.5 22.3 + - + -
42E VAL* 5.0 7.9 - - + +
43E SER* 5.1 4.8 + - - -
289E PHE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.3 23.0 - - - -
40B ILE* 3.1 32.7 + - + +
45B THR* 4.2 2.3 - - + +
46B LYS* 1.3 73.8 - - - +
48B LEU* 1.3 61.5 + - - +
124B VAL* 5.1 0.4 - - + -
125B GLN 3.7 5.2 - - - -
126B VAL* 4.5 3.8 - - + +
136B ALA* 3.8 26.0 - - + +
137B CYS* 4.1 19.3 - - - +
140B ALA* 4.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 5.2 1.8 - - + -
31B PHE* 3.7 34.5 - - + -
38B ALA 3.9 12.3 - - - +
39B TYR* 4.2 9.2 - - + +
47B ALA* 1.3 78.8 - - - +
49B ALA* 1.3 70.3 + - - +
50B VAL* 4.1 9.0 - - + -
123B TYR 3.9 0.2 - - - +
124B VAL* 3.4 4.1 - - - +
125B GLN* 2.9 43.4 + - + +
127B LEU* 4.5 11.7 - - + -
140B ALA* 4.8 1.6 - - - -
88E SER* 5.0 4.5 + - - +
142E LEU* 4.7 16.8 - - + -
289E PHE* 4.0 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 3.8 1.0 - - - -
38B ALA* 3.4 27.2 + - + +
48B LEU* 1.3 75.6 - - - +
50B VAL* 1.3 74.8 + - - +
122B ILE* 5.8 0.2 - - + -
123B TYR 3.3 8.5 - - - +
124B VAL* 4.6 4.7 - - + +
140B ALA* 3.4 39.1 - - + +
141B ALA* 3.5 14.6 - - + +
144B ALA* 4.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 4.5 13.7 - - + -
34B ALA* 4.0 9.6 - - + -
36B GLY 3.5 13.2 - - - +
37B SER* 4.6 1.8 - - - +
48B LEU* 4.1 11.7 - - + -
49B ALA* 1.3 87.5 - - - +
51B VAL* 1.3 72.0 + - - +
52B TYR* 3.3 38.4 - - + +
121B ASP 3.7 0.6 - - - +
122B ILE* 3.4 1.0 - - - +
123B TYR* 2.9 35.4 + - + +
144B ALA* 4.7 0.2 - - - -
88E SER* 3.9 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 3.7 4.0 - - - +
36B GLY* 3.0 41.1 + - - +
50B VAL* 1.3 81.5 - - - +
52B TYR* 1.3 65.8 + - - +
53B GLY* 3.4 3.5 + - - -
120B ILE* 5.5 1.6 - - + -
121B ASP 3.2 5.8 - - - +
122B ILE* 3.9 26.5 - - + -
141B ALA* 4.5 1.3 - - - +
144B ALA* 3.6 31.2 - - + +
145B VAL* 4.0 14.4 - - + +
148B ALA* 3.6 12.1 - - + +
150B ILE* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 4.3 9.1 + - - +
34B ALA* 3.9 26.9 - - + +
35B ASP* 4.5 6.5 - - - +
50B VAL* 3.3 25.4 - - + +
51B VAL* 1.3 69.8 - - - +
53B GLY* 1.3 70.4 + - - +
55B HIS* 3.9 10.0 + - + +
120B ILE* 3.9 1.2 - - - +
121B ASP* 2.9 39.5 + - + +
123B TYR* 3.7 27.8 - + - -
87E ALA 4.3 4.7 - - - -
88E SER 2.6 27.5 + - - -
89E ALA 3.2 13.9 + - - -
91E PRO* 4.2 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 3.3 25.1 + - - -
51B VAL 3.4 6.2 + - - -
52B TYR* 1.3 78.9 - - - +
54B PRO* 1.3 65.3 - - - -
55B HIS* 2.6 17.7 + - - -
119B GLN 2.6 20.6 - - - +
120B ILE* 4.4 2.7 - - - -
148B ALA* 5.6 1.1 - - - -
150B ILE* 4.5 9.0 - - - -
75H ARG* 4.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY* 1.3 81.2 - - - +
55B HIS* 1.3 58.2 + - - +
115B HIS* 4.2 35.2 - - + +
118B SER* 4.2 11.2 - - - -
119B GLN 3.0 10.8 - - - +
120B ILE* 4.0 13.4 - - + -
148B ALA 5.7 1.3 - - - +
150B ILE* 4.1 22.7 - - + -
75H ARG* 3.7 18.2 + - + -
103H ARG* 3.0 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 3.9 14.6 + - + +
53B GLY 2.6 28.1 + - - +
54B PRO* 1.3 74.8 - - - +
56B GLU* 1.3 81.5 + - - +
58B ARG* 3.4 23.1 + - - -
118B SER* 3.3 8.0 - - - -
119B GLN* 3.0 44.9 + - - -
121B ASP* 3.0 29.8 + - + -
91E PRO* 5.1 6.4 - - + +
75H ARG* 4.1 20.4 - - - +
102H SER 4.6 1.8 - - - +
103H ARG 3.9 11.0 - - - -
----------------------------------------------------------
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