Contacts of the strand formed by residues 114 - 118 (chain A) in PDB entry 1XT9
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 SER 114 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 3.9 3.1 - - - -
109A LEU 3.1 26.7 + - - +
112A LYS 3.3 8.7 - - - -
113A ASN* 1.3 79.2 - - - +
115A PHE* 1.3 77.2 + - - +
116A PHE* 3.5 20.7 - - - -
147A LEU* 3.8 6.6 - - - +
148A ALA* 3.2 23.2 + - - -
150A VAL* 3.2 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.9 0.9 - - + -
106A LEU* 3.5 40.4 - - + -
107A VAL 3.3 3.8 - - - -
108A TYR* 3.8 31.0 - + + -
114A SER* 1.3 80.4 + - - +
116A PHE* 1.3 60.9 + - - +
133A ALA* 3.8 36.6 - - + -
136A LEU* 4.3 16.4 - - + -
140A LEU* 4.2 13.0 - - + -
147A LEU* 3.8 36.3 - - + -
148A ALA 2.8 14.6 + - - +
149A PHE* 4.0 14.8 - + + -
150A VAL* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 3.5 3.3 - - - +
107A VAL* 2.6 49.4 + - + +
109A LEU* 3.6 31.2 - - + -
112A LYS* 3.7 23.6 - - + -
114A SER* 3.5 35.0 - - - -
115A PHE* 1.3 74.8 - - - +
117A HIS* 1.3 60.0 + - - +
118A TYR* 3.8 21.5 - + + -
150A VAL* 3.4 24.5 - - + -
152A GLU* 3.1 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 4.6 0.6 - - + +
104A SER* 2.4 34.9 + - - -
105A LEU 3.3 17.3 - - - -
106A LEU* 4.3 4.7 - - + -
116A PHE* 1.3 72.6 - - - +
118A TYR* 1.3 61.3 + - - +
119A ASP* 3.7 14.1 + - + +
125A ASN* 3.6 22.1 - - - +
126A SER 3.8 0.7 - - - -
129A ALA* 3.3 31.7 - - + +
149A PHE* 3.9 12.3 - - + -
150A VAL 2.9 13.7 + - - +
151A GLU* 2.7 35.7 + - - +
152A GLU* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 3.6 1.9 + - - -
105A LEU* 2.9 44.3 + - + +
107A VAL* 4.1 15.0 - - + -
109A LEU* 6.2 0.3 - - - +
116A PHE* 3.8 29.7 - - + +
117A HIS* 1.3 75.0 - - - +
119A ASP* 1.3 58.7 + - - +
120A SER 4.1 1.3 + - - -
152A GLU* 3.8 25.1 - - + +
153A LYS 4.9 3.6 - - - -
154A ALA* 3.8 24.0 - - + -
167A VAL* 5.3 1.4 - - - +
170A ASN* 3.9 19.6 - - - +
174A LEU* 3.8 28.3 - - + +
178A PHE* 5.8 0.7 - - - -
186A LEU* 3.5 29.1 - - + +
----------------------------------------------------------
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