Contacts of the strand formed by residues 87 - 92 (chain L) in PDB entry 6VEN
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 87 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L LEU* 5.8 4.4 - - - +
82L ILE* 3.5 9.9 - - - -
83L HIS* 2.9 29.6 + - - +
85L SER 3.5 3.0 + - - -
86L TYR* 1.3 82.4 - - - +
88L LEU* 1.3 65.8 + - - -
89L LEU* 3.9 0.5 - - - +
339R GLN* 4.6 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L THR 5.5 0.7 - - - -
53L SER* 3.7 30.3 - - - +
80L GLU* 3.2 26.5 - - + +
81L ILE 4.2 2.5 - - - +
82L ILE* 3.5 32.4 - - + +
86L TYR 4.1 2.6 - - - +
87L GLY* 1.3 74.4 - - - +
89L LEU* 1.3 73.6 + - - +
91L THR* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L CYS* 4.1 11.0 - - - -
81L ILE* 2.9 19.9 + - + +
83L HIS* 3.5 33.4 - - + +
86L TYR* 4.7 5.2 - - + +
87L GLY 3.5 3.1 + - - +
88L LEU* 1.3 87.7 - - - +
90L HIS* 1.3 81.6 + - + +
91L THR* 5.5 0.2 - - - +
417M TYR* 4.0 24.5 - - + +
420M ILE* 4.7 19.2 - - + +
421M ILE* 4.0 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L VAL 3.9 0.5 - - - +
80L GLU* 2.9 12.5 - - - +
81L ILE* 3.0 45.8 + - + +
89L LEU* 1.3 95.0 + - + +
91L THR* 1.3 66.0 + - - +
92L PHE* 3.9 13.0 - - + -
125L THR 3.5 15.0 - - - -
126L LEU* 3.3 24.6 + - - -
127L ASN 4.4 2.0 - - - -
128L GLY* 3.7 17.0 - - - -
420M ILE* 3.4 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L SER* 5.9 1.1 - - - +
79L VAL 3.7 0.4 - - - -
80L GLU* 3.0 32.1 - - - +
88L LEU* 3.7 17.9 - - + -
89L LEU 5.5 0.2 - - - +
90L HIS* 1.3 75.5 - - - +
92L PHE* 1.3 66.2 + - - +
93L ILE* 3.4 23.7 + - - +
128L GLY 5.1 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77L PHE 4.7 0.3 - - - +
78L SER* 3.3 4.2 - - - -
79L VAL* 2.9 63.9 + - + +
81L ILE* 3.6 31.6 - - + -
90L HIS* 3.9 7.9 - - + -
91L THR* 1.3 70.2 - - - +
93L ILE* 1.3 58.9 + - - +
94L GLY 3.6 2.9 + - - -
95L HIS* 5.4 0.7 + - - -
111L LEU* 4.3 20.0 - - + -
123L TRP* 3.8 40.9 - + + -
124L ASP 3.8 11.2 - - - -
125L THR* 4.3 12.3 - - - -
128L GLY* 3.3 43.1 - - - -
----------------------------------------------------------
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