Contacts of the strand formed by residues 72 - 81 (chain H) in PDB entry 4BEI
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 VAL 72 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PRO* 4.8 19.1 - - + -
39H VAL 6.2 0.4 - - - -
40H ILE* 3.8 29.2 - - + -
66H ASN* 3.4 34.0 - - + +
68H SER* 4.5 4.9 - - - +
71H THR* 1.3 75.8 + - - +
73H LYS* 1.3 71.9 + - - +
74H PHE* 3.9 5.2 - - + -
105H ALA* 3.3 5.0 - - - +
106H LEU* 2.9 40.9 + - + +
137H ALA* 4.7 10.5 - - + -
138H GLU* 5.3 2.7 - - + +
139H ASN* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ASN* 3.2 24.8 + - - +
71H THR 4.3 0.4 + - - -
72H VAL* 1.3 80.0 - - - +
74H PHE* 1.3 62.8 + - - +
103H SER* 3.3 25.0 - - - +
104H ASP 3.1 18.2 - - - +
105H ALA* 4.3 5.6 - - + +
138H GLU* 2.9 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ILE* 4.0 13.7 - - + -
64H ILE* 3.9 25.4 - - + -
72H VAL* 3.9 6.7 - - + -
73H LYS* 1.3 79.7 - - - +
75H LYS* 1.3 68.5 + - - +
76H TYR* 3.7 24.0 - + + -
103H SER* 4.2 3.1 + - - -
104H ASP* 2.7 52.5 + - + +
105H ALA* 3.9 12.8 - - - -
106H LEU* 3.9 32.1 - - + -
112H LEU* 4.3 9.0 - - + -
135H VAL* 3.8 21.5 - - + -
136H VAL 3.4 12.6 - - - +
137H ALA* 3.8 10.1 - - + +
138H GLU* 4.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237G ASN* 5.8 2.1 - - - +
239G ASP* 3.4 35.1 + - - -
241G SER* 4.9 4.0 - - - +
242G TYR* 4.0 24.9 - - + +
74H PHE* 1.3 74.7 - - - +
76H TYR* 1.3 61.2 + - - +
77H TRP* 4.1 14.7 - - + -
101H GLN* 2.8 30.7 + - + +
102H GLU* 3.9 12.1 - - - +
103H SER* 3.4 30.9 + - - +
135H VAL* 3.5 1.9 - - - +
136H VAL* 2.7 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H LEU* 3.9 22.0 - - + -
64H ILE* 3.7 24.5 - - + -
74H PHE* 3.7 18.2 - + + -
75H LYS* 1.3 77.2 - - - +
77H TRP* 1.3 75.2 + - - +
101H GLN* 3.4 14.7 + - - -
102H GLU 4.9 2.5 + - - +
104H ASP* 3.7 26.1 + - + -
112H LEU* 4.0 13.1 - - + +
114H VAL* 3.7 23.4 - - + +
116H ARG* 4.0 19.2 + - - -
133H LEU* 3.9 10.1 - - + -
134H GLN 3.2 13.7 - - - +
135H VAL* 4.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G LEU* 4.1 8.7 - - + -
213G ILE 3.2 18.6 + - - -
214G ILE* 3.6 28.3 - - + -
215G PRO* 3.5 22.0 - - + -
242G TYR* 3.9 17.0 - + - -
75H LYS* 4.1 15.9 - - + -
76H TYR* 1.3 95.3 - - - +
78H LEU* 1.3 60.3 + - - +
79H SER* 3.6 9.4 - - - -
101H GLN* 3.6 39.7 - - + +
116H ARG* 4.6 7.9 - - - +
133H LEU* 3.8 4.3 - - - +
134H GLN* 3.0 59.5 + - + +
136H VAL* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G PRO* 4.7 2.3 - - - +
44H LEU* 4.2 3.4 - - + -
60H SER* 3.8 20.6 - - - +
62H LEU* 4.0 19.7 - - + -
77H TRP* 1.3 75.7 - - - +
79H SER* 1.3 64.1 + - - +
89H PRO* 3.9 3.5 - - - +
90H ALA* 2.9 42.1 + - + +
91H LYS* 4.4 1.4 + - - +
116H ARG* 3.8 33.5 + - + +
118H PHE* 4.4 13.0 - - + -
131H VAL* 3.8 15.7 - - + -
132H SER 3.7 14.8 - - - +
133H LEU* 3.7 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205G THR* 5.7 0.3 - - - +
213G ILE* 2.7 50.8 + - - +
215G PRO* 3.8 9.7 - - - +
77H TRP* 3.6 8.6 - - - -
78H LEU* 1.3 76.6 + - - +
80H ILE* 1.3 64.1 + - - +
81H LYS 4.4 0.2 + - - -
88H PHE 3.8 5.8 - - - -
89H PRO* 4.4 1.7 - - - +
90H ALA 4.3 0.2 - - - +
130H THR 3.9 0.3 - - - +
131H VAL* 3.6 1.7 - - - -
132H SER* 2.8 44.3 + - - -
134H GLN* 5.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G ILE* 4.6 5.2 - - - +
79H SER* 1.3 83.5 - - - +
81H LYS* 1.3 63.1 + - - +
82H GLY 4.3 0.2 - - - -
87H TYR* 3.5 4.3 - - - +
88H PHE* 2.8 86.3 + - + +
90H ALA* 4.2 14.6 - - + -
118H PHE* 3.8 17.5 - - + -
129H TYR* 3.8 19.1 - - + -
130H THR 3.5 7.4 - - - +
131H VAL* 3.7 30.5 - - + -
149H PHE* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G ILE* 4.0 13.4 - - + +
80H ILE* 1.3 76.0 - - - +
82H GLY* 1.3 65.7 + - - +
85H GLY* 6.6 0.2 - - - -
86H ILE 3.5 10.8 - - - +
87H TYR* 3.6 21.8 - - + -
128H LYS 4.4 0.2 - - - +
129H TYR* 3.4 3.7 - - - -
130H THR* 2.7 49.8 + - - +
248H THR* 4.5 0.2 - - - +
1272H O4B 2.7 111.0 + - - +
----------------------------------------------------------
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