Contacts of the strand formed by residues 102 - 108 (chain B) in PDB entry 4X61
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 ALA 102 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL 3.8 0.2 - - - +
98B SER* 3.0 32.4 + - - -
100B SER* 3.2 17.3 + - - +
101B GLY* 1.3 78.5 - - - +
103B VAL* 1.3 61.6 - - - +
104B GLU* 4.7 0.9 - - - +
120B CYS* 4.4 11.0 - - - -
121B LYS 3.4 15.0 - - - +
122B TYR* 3.5 25.1 - - + -
128B VAL* 3.6 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.7 27.8 - - + -
96B VAL 3.4 5.6 - - - +
101B GLY 4.4 0.2 + - - -
102B ALA* 1.3 73.4 - - - +
104B GLU* 1.3 63.0 + - - +
119B PHE* 3.7 14.4 - - + -
121B LYS* 3.0 29.9 + - - +
124B HIS* 4.6 2.0 - - + -
128B VAL* 3.8 19.7 - - + +
131B VAL* 4.4 6.5 - - + -
142B SER* 3.8 29.2 - - - +
152B TRP* 3.7 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 5.0 6.0 - - - +
80B GLU* 4.0 16.0 + - - +
81B ALA 5.8 0.2 + - - -
94B ILE 3.7 0.5 - - - +
95B LEU* 3.6 4.0 - - - +
96B VAL* 2.7 54.0 + - + +
98B SER* 3.8 20.6 + - - -
100B SER* 4.4 0.5 + - - -
102B ALA* 4.7 2.4 - - - +
103B VAL* 1.3 76.9 - - - +
105B LEU* 1.3 57.8 + - - +
106B TRP* 3.2 36.9 + - + +
117B SER* 5.1 1.7 + - - +
119B PHE* 3.2 20.2 - - - +
120B CYS* 3.7 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 4.1 22.7 - - + -
93B GLY* 4.2 7.2 - - - -
94B ILE 3.4 29.6 - - - +
95B LEU* 4.1 5.6 - - + +
104B GLU* 1.3 72.2 - - - +
106B TRP* 1.3 59.8 + - - +
107B GLU* 5.3 5.6 - - - +
117B SER* 3.8 1.7 + - - -
118B LYS* 2.7 48.1 + - + +
119B PHE* 2.9 48.7 + - + +
154B LEU* 4.2 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.6 24.3 - - + +
77B VAL* 3.7 27.1 - - + -
78B GLN 3.9 17.9 - - - -
79B THR* 3.7 19.3 - - + +
80B GLU 5.7 0.2 - - - -
92B ARG 3.7 0.3 - - - +
93B GLY* 3.6 3.3 - - - -
94B ILE* 2.8 49.2 + - + +
96B VAL* 3.8 14.3 - - + +
104B GLU* 3.2 36.0 + - - +
105B LEU* 1.3 80.5 - - - +
107B GLU* 1.3 61.6 + - - +
108B LEU 3.8 0.3 + - - -
115B ILE* 3.7 22.7 - - + -
116B VAL* 3.4 7.2 - - - -
117B SER* 3.3 42.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 3.5 16.1 - - - +
93B GLY* 3.9 9.4 + - - -
105B LEU* 4.1 7.6 + - - +
106B TRP* 1.3 71.8 - - - +
108B LEU* 1.3 71.7 + - - +
115B ILE* 3.9 1.7 - - - -
116B VAL* 2.6 50.2 + - + +
118B LYS* 4.1 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 3.6 27.8 - - - +
60B LEU* 3.8 27.4 - - + -
75B ALA* 4.6 1.6 - - + -
88B TRP* 4.3 17.0 - - + -
92B ARG* 2.7 37.3 + - + +
94B ILE* 5.1 7.6 - - + +
106B TRP 3.8 0.8 + - - -
107B GLU* 1.3 82.8 - - - +
109B ASP* 1.3 71.9 + - - +
110B GLU 3.8 0.2 + - - -
112B GLU* 4.1 15.9 - - + +
114B LEU 3.4 18.8 - - - +
115B ILE* 3.8 20.6 - - + +
116B VAL* 5.6 0.7 - - - -
----------------------------------------------------------
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