Contacts of the strand formed by residues 119 - 122 (chain B) in PDB entry 1SXG
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 119 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR 3.8 2.2 + - - -
63B VAL* 3.5 1.4 - - - +
64B GLY 3.0 21.5 + - - -
117B VAL* 3.2 4.4 - - - +
118B ASP* 1.3 79.1 - - - +
120B ILE* 1.3 67.8 + - - +
140B VAL* 4.8 0.4 - - - -
141B PRO 3.4 10.3 - - - -
305B LEU* 3.9 13.2 - - - -
309B MET* 3.4 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 3.0 9.0 - - - +
66B ILE* 4.8 10.1 - - + -
109B LEU* 4.7 9.0 - - + +
112B MET* 3.1 41.1 - - + -
113B LEU* 4.3 10.1 - - + -
117B VAL* 3.8 9.6 - - + -
119B GLY* 1.3 80.6 - - - +
121B ILE* 1.3 74.6 + - - +
122B PHE* 4.2 5.2 - - + -
140B VAL* 4.6 5.8 - - + -
141B PRO 2.9 11.6 + - - +
142B VAL* 3.0 27.5 - - + -
143B VAL 2.8 25.8 + - - -
305B LEU* 3.2 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.6 20.6 - - + -
64B GLY 2.9 6.6 + - - +
65B VAL* 3.3 12.0 - - + +
66B ILE 3.3 21.5 + - - -
82B ILE* 4.2 16.4 - - + -
120B ILE* 1.3 78.1 - - - +
122B PHE* 1.3 62.3 + - - +
123B MET* 3.9 17.5 - - + -
143B VAL* 3.4 15.5 - - + +
145B ALA* 3.8 27.4 - - + -
298B GLY 5.5 0.9 - - - +
301B ALA* 4.8 12.6 - - + +
302B MET* 4.0 13.5 - - - +
305B LEU* 3.3 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 3.2 34.8 - - + -
98B SER* 5.6 1.3 - - - -
105B GLU* 3.8 28.9 - - + -
109B LEU* 6.6 0.2 - - + -
120B ILE* 3.9 3.6 - - + -
121B ILE* 1.3 76.2 - - - +
123B MET* 1.3 74.8 + - - +
124B SER* 3.3 28.0 - - - -
127B VAL* 4.4 13.2 - - + -
131B HIS* 4.7 10.5 - + - -
135B LEU* 4.5 14.6 - - + -
142B VAL* 3.8 20.2 - - + -
143B VAL 2.9 8.3 + - - +
144B LEU* 3.1 37.4 - - + +
145B ALA 3.1 21.3 + - - -
----------------------------------------------------------
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