Contacts of the strand formed by residues 92 - 99 (chain B) in PDB entry 3EYF
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 GLY 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 4.8 1.3 - - - -
39B GLN 3.3 12.8 - - - -
41B PRO* 4.1 5.4 - - - -
90B ASP 3.4 3.1 + - - -
91B MET* 1.3 77.4 - - - +
93B LEU* 1.3 62.4 - - - -
94B TYR* 3.5 9.6 - - - -
120B MET* 3.3 13.9 - - - +
121B VAL 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY* 6.1 5.2 - - - -
37B VAL 3.9 0.5 - - - +
38B ARG* 3.3 4.3 - - - -
39B GLN* 2.9 40.2 + - + +
92B GLY* 1.3 74.2 - - - -
94B TYR* 1.3 62.2 + - - +
95B TYR* 3.3 36.1 + - + +
117B GLN 4.2 6.1 - - - +
118B GLY* 4.1 12.6 - - - +
119B THR 3.7 17.7 - - - -
120B MET* 3.3 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 3.8 1.6 - - - +
20B LEU* 3.7 26.2 - - + -
36B TRP* 3.8 18.6 - + + -
37B VAL 3.6 2.7 - - - -
38B ARG* 3.3 28.6 + - + -
48B LEU* 3.4 28.0 - - + -
68B PHE* 4.0 1.6 - + - -
81B LEU* 4.8 3.1 - - + -
83B MET* 3.8 24.9 - - - -
90B ASP* 2.7 36.5 + - - +
92B GLY 3.5 15.0 - - - -
93B LEU* 1.3 73.9 - - - +
95B TYR* 1.3 63.3 + - - +
118B GLY* 3.1 3.6 - - - -
119B THR* 2.8 35.4 + - + +
121B VAL* 3.5 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 3.4 12.6 + + - -
41A GLY* 5.9 1.2 + - - -
42A GLN 4.7 2.8 + - - -
44A PRO* 3.9 20.6 - - + -
6B GLU* 3.2 5.6 - - - +
36B TRP* 3.2 9.2 - - - -
37B VAL* 2.7 50.7 + - - +
39B GLN* 3.0 29.4 + - + -
45B LEU* 4.0 24.7 - - + -
93B LEU* 3.3 24.3 - - + +
94B TYR* 1.3 73.5 - - - +
96B CYS* 1.3 61.7 + - - +
97B ALA* 3.9 0.5 + - - +
115B TRP* 4.2 24.2 - + + -
116B GLY 3.2 19.3 - - - +
117B GLN 3.0 27.4 - - - -
118B GLY* 3.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.8 20.3 - - - +
5B VAL 4.6 1.3 - - - -
6B GLU* 2.6 23.6 + - - +
22B CYS* 2.0 54.7 - - + -
34B ILE* 4.3 2.7 - - + -
35B HIS 3.2 9.0 - - - +
36B TRP* 3.9 13.2 - - + -
95B TYR* 1.3 74.1 - - - +
97B ALA* 1.3 60.2 + - - +
115B TRP* 3.6 0.9 - - - +
116B GLY 3.0 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.2 0.7 - - - -
34B ILE* 3.7 4.2 - - - +
35B HIS* 2.7 42.9 + - + +
37B VAL* 5.4 1.3 - - + -
95B TYR 4.8 2.7 - - - +
96B CYS* 1.3 77.7 - - - +
98B ARG* 1.3 63.7 + - - +
112B LEU* 3.6 29.8 - - + -
114B TYR 3.3 9.9 - - - +
115B TRP* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 4.2 9.4 - - - +
4B LEU* 3.8 10.7 - - + +
27B PHE* 3.2 57.4 - - + +
32B HIS* 3.5 32.0 + - + -
33B GLY 4.0 3.4 - - - +
34B ILE* 4.3 7.9 - - + -
35B HIS* 4.4 0.2 - - - -
97B ALA* 1.3 72.5 - - - +
99B ASP* 1.3 70.9 + - - +
111B LEU 3.2 2.4 - - - +
112B LEU* 3.2 4.3 - - - -
113B ASP* 2.9 60.2 + - - +
114B TYR* 2.8 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 2.9 28.1 - - - +
33B GLY* 2.8 33.1 + - - +
35B HIS* 3.0 26.8 + - - +
97B ALA 3.6 1.6 + - - -
98B ARG* 1.3 71.8 - - - +
100B GLY* 1.3 66.2 + - - +
102B CYS* 4.6 2.8 - - - -
107B CYS 4.8 0.2 - - - +
108B TYR* 3.3 18.0 - - + +
109B SER* 2.8 26.7 + - - -
110B GLY* 2.8 25.1 + - - -
111B LEU 3.3 4.0 + - - -
113B ASP* 3.9 0.2 - - - -
----------------------------------------------------------
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