Contacts of the strand formed by residues 93 - 101 (chain B) in PDB entry 2X5Q
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 ASN 93 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU* 4.5 7.3 + - - +
89B ILE* 4.2 1.2 - - - +
92B GLY* 1.3 80.0 - - - +
94B HIS* 1.3 64.8 + - - +
122B PRO* 3.4 9.4 - - - +
123B ILE* 3.3 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 3.5 33.7 + - + +
92B GLY 3.8 9.6 + - - -
93B ASN* 1.3 81.1 - - - +
95B PHE* 1.3 60.8 + - - +
96B LYS* 4.4 10.0 + - + -
120B SER* 4.5 11.0 - - - -
121B LEU 3.2 4.5 - - - -
123B ILE* 4.0 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 4.3 16.8 - - + -
74A PHE* 3.7 27.1 - + - -
132A GLN 4.3 17.9 - - - +
133A VAL* 4.1 20.9 - - + -
61B TYR* 5.6 3.4 - - - -
94B HIS* 1.3 73.9 - - - +
96B LYS* 1.3 59.3 + - - +
97B ILE* 3.4 24.5 - - + +
120B SER* 3.2 2.7 - - - -
121B LEU* 2.9 38.1 + - + +
123B ILE* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLN* 3.1 37.8 - - + +
133A VAL 2.9 26.0 + - - +
9B GLU* 3.2 32.5 + - - +
94B HIS* 4.2 10.9 - - + -
95B PHE* 1.3 74.0 - - - +
97B ILE* 1.3 64.4 + - - +
98B ILE* 4.1 7.4 + - + +
118B THR* 4.1 20.0 - - + -
119B PHE 3.6 5.4 - - - +
120B SER* 3.5 21.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
74A PHE* 3.5 24.7 - - + -
133A VAL* 3.5 9.2 - - + -
135A LEU* 3.8 28.5 - - + -
95B PHE* 3.4 30.3 - - + +
96B LYS* 1.3 72.1 - - - +
98B ILE* 1.3 62.5 + - - +
100B ILE* 3.9 17.5 - - + -
118B THR* 3.2 5.9 - - - +
119B PHE* 2.7 64.0 + - + +
121B LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLN* 3.5 27.1 - - + +
133A VAL 2.8 18.0 + - - +
134A ASP* 3.9 22.2 - - + +
135A LEU* 3.0 22.5 + - - +
136A ARG* 3.4 40.0 + - - +
96B LYS* 4.4 14.6 - - + +
97B ILE* 1.3 73.2 - - - +
99B GLY* 1.3 68.4 + - - +
100B ILE 3.2 3.1 + - - -
118B THR* 3.6 13.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
135A LEU 3.2 18.5 - - - +
136A ARG* 3.5 19.1 + - - +
98B ILE* 1.3 71.7 - - - +
100B ILE* 1.3 63.9 + - - +
101B PRO* 3.6 2.3 - - - +
116B ASN* 3.8 23.7 + - - +
117B ILE 3.2 9.8 + - - -
118B THR* 3.0 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR 3.0 28.5 - - - +
74A PHE* 4.0 4.5 - - + +
135A LEU* 3.6 25.4 - - + -
97B ILE* 3.9 4.9 - - + -
98B ILE 3.2 2.8 + - - -
99B GLY* 1.3 75.7 - - - +
101B PRO* 1.3 81.2 - - + +
102B SER 3.2 0.3 + - - -
104B LYS* 4.3 13.5 - - + -
105B LEU* 3.8 42.8 - - + -
116B ASN* 2.9 0.8 - - - +
117B ILE 2.8 45.0 + - - +
119B PHE* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.8 13.5 - - + +
137A ASP 6.2 0.9 - - - +
138A LYS 5.2 7.9 - - - +
99B GLY 3.6 6.9 - - - +
100B ILE* 1.3 96.1 - - + +
102B SER* 1.3 66.7 + - - +
103B ASN* 3.1 18.4 - - - +
104B LYS* 3.1 35.4 + - + +
105B LEU 4.0 1.7 + - - -
115B GLY 4.0 2.0 - - - +
116B ASN* 3.7 10.5 - - + +
----------------------------------------------------------
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