Contacts of the strand formed by residues 96 - 102 (chain B) in PDB entry 6XAV
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 THR 96 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 5.5 1.3 - - + -
53B GLY* 3.8 17.0 - - - +
54B VAL* 4.8 10.6 - - + +
94B GLY 3.3 8.3 + - - -
95B ASP* 1.3 68.9 - - - +
97B ILE* 1.3 60.8 + - - +
98B SER* 4.3 14.1 - - - +
118B GLU 3.5 1.7 - - - +
119B VAL* 3.4 7.1 - - - -
120B ASN* 2.7 46.9 + - - +
121B PHE* 3.6 38.3 - - + +
249B LYS* 5.0 7.3 - - - +
253B LEU* 5.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 3.3 20.6 - - - -
53B GLY 3.3 10.3 + - - +
55B LEU* 4.7 5.8 - - + -
65B LEU* 4.0 26.3 - - + +
81B VAL* 6.0 1.1 - - + -
91B LEU* 3.8 39.9 - - + -
95B ASP* 3.3 15.5 + - + +
96B THR* 1.3 79.3 - - - +
98B SER* 1.3 68.1 + - - +
113B LEU* 3.7 30.5 - - + -
116B VAL* 3.8 21.1 - - + -
118B GLU 3.8 0.9 - - - -
119B VAL* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLY 3.4 11.2 - - - -
52B ASP* 3.3 19.1 - - - +
96B THR* 4.3 10.9 - - - +
97B ILE* 1.3 75.4 - - - +
99B GLY* 1.3 56.9 + - - +
117B ASN* 2.9 24.8 + - - +
118B GLU* 3.0 34.5 + - - +
121B PHE* 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.7 7.9 - - - +
51B GLY 3.2 27.2 + - - +
97B ILE 4.2 0.4 - - - -
98B SER* 1.3 75.6 - - - +
100B LYS* 1.3 67.4 + - - -
101B ILE* 3.5 4.0 + - - +
113B LEU* 4.1 11.6 - - - +
115B LYS 3.3 14.4 - - - -
116B VAL* 4.2 0.4 - - - -
117B ASN* 3.6 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 3.0 43.6 + - + +
49B ILE 3.4 13.5 - - - +
50B PHE* 3.7 24.8 - - + -
99B GLY* 1.3 71.4 - - - -
101B ILE* 1.3 65.3 + - - +
113B LEU* 3.4 8.1 - - - +
114B LEU* 3.3 37.2 + - + +
115B LYS* 3.2 19.0 + - + +
117B ASN* 3.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.7 8.1 - - + -
39B LEU* 5.4 1.1 - - + -
48B ASP* 5.3 0.2 - - - -
49B ILE* 2.6 58.2 + - + +
50B PHE 3.9 5.8 - - - +
51B GLY* 3.8 23.8 - - - +
65B LEU* 5.7 1.3 - - + -
79B ILE* 3.8 44.6 - - + -
99B GLY 3.8 9.0 - - - +
100B LYS* 1.3 83.7 - - - +
102B ARG* 1.3 61.5 + - - +
111B PHE* 4.3 17.9 - - + -
112B ALA 3.3 9.0 - - - +
113B LEU* 4.3 5.2 - - + -
114B LEU* 3.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 5.3 0.2 - - - -
101B ILE* 1.3 76.2 - - - +
103B PRO* 1.3 82.0 + - + +
104B PRO* 4.8 0.2 - - - +
105B LYS* 3.3 42.3 - - - +
108B GLU* 3.3 32.1 + - - -
111B PHE* 3.2 25.8 - - - -
112B ALA* 3.2 31.1 + - + +
114B LEU* 3.7 32.8 - - + +
----------------------------------------------------------
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