Contacts of the strand formed by residues 74 - 78 (chain B) in PDB entry 5DQZ
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 LEU 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO* 4.2 6.5 - - + -
50B ALA 3.4 14.3 + - - +
51B CYS* 3.6 3.1 - - - -
52B ILE* 3.0 26.0 + - - +
72B GLY 3.9 2.8 + - - -
73B THR* 1.3 75.3 - - - +
75B LEU* 1.3 62.3 + - - +
76B VAL* 3.8 23.6 - - + -
87B ALA* 4.3 2.7 - - + -
88B SER 3.2 25.6 - - - +
89B GLY* 4.4 3.4 - - - +
189B GLY 4.0 5.6 - - - +
192B GLU* 3.9 21.3 - - + -
193B ALA* 3.8 31.0 - - + +
196B LEU* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 4.3 8.5 - - + -
52B ILE* 3.6 36.3 - - + -
54B LEU* 4.4 13.5 - - + -
60B VAL* 4.6 5.4 - - + -
64B ALA 4.8 0.7 - - - +
65B VAL* 4.1 32.8 - - + -
68B ALA* 3.7 34.1 - - + -
73B THR* 3.5 0.8 + - + +
74B LEU* 1.3 74.3 - - - +
76B VAL* 1.3 59.9 - - - +
77B TRP* 4.2 21.1 - - + -
87B ALA* 3.2 7.3 - - - +
88B SER* 2.9 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS* 3.5 28.0 - - - -
52B ILE 2.8 8.9 + - - -
53B MET* 3.3 17.9 - - - -
54B LEU* 2.8 26.4 + - - +
74B LEU* 3.8 18.6 - - + -
75B LEU* 1.3 79.4 - - - +
77B TRP* 1.3 63.5 + - - +
78B VAL* 3.5 16.0 + - + +
84B ARG* 3.9 26.0 - - + +
86B TYR 3.5 9.9 - - - +
87B ALA* 4.6 2.9 - - + -
185B SER 6.2 0.2 - - - +
189B GLY* 4.7 8.7 - - - -
192B GLU* 5.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 5.1 4.2 + - + -
61A SER 5.1 0.2 + - - -
62A HIS* 3.6 34.2 - + + +
65A VAL* 3.5 46.7 - - + +
77A TRP* 4.0 21.5 - + - -
54B LEU* 3.5 34.6 - - + +
58B THR* 4.9 2.0 + - - -
60B VAL* 4.2 19.1 - - + +
65B VAL* 4.7 1.8 - - + -
75B LEU* 4.2 15.9 - - + -
76B VAL* 1.3 70.9 - - - +
78B VAL* 1.3 54.7 + - - +
84B ARG* 4.1 0.3 - - - -
85B VAL* 2.8 34.3 + - + +
86B TYR* 2.9 35.3 + + + +
87B ALA 4.2 1.6 - - - -
88B SER* 3.4 36.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS* 2.7 23.4 + - - -
19B PHE* 4.7 13.0 - - + -
53B MET* 4.5 14.1 - - + -
54B LEU 3.0 18.5 + - - +
55B GLU* 4.2 15.7 - - + -
56B PRO* 3.4 5.9 - - - +
76B VAL* 3.5 22.0 + - + +
77B TRP* 1.3 79.3 - - - +
79B GLY* 1.3 64.4 + - - +
82B GLY* 4.0 15.0 - - - +
83B VAL 3.2 14.8 - - - +
84B ARG* 4.0 5.8 - - - -
85B VAL* 4.0 2.2 - - - +
185B SER* 4.4 3.6 - - - +
248B ARG* 5.8 0.4 - - - +
----------------------------------------------------------
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