Contacts of the strand formed by residues 87 - 94 (chain A) in PDB entry 1XYY
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 LYS 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP 3.5 19.2 + - - +
52A LEU* 3.4 13.8 - - + +
53A VAL 2.9 23.9 + - - -
85A GLY 3.6 3.5 + - - +
86A ARG* 1.3 75.1 - - - +
88A VAL* 1.3 60.2 + - - +
118A GLU* 3.3 34.4 + - - +
120A VAL* 3.8 9.0 - - + -
147A ALA 5.2 0.9 - - - -
148A ILE* 3.3 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 5.1 2.7 - - + -
52A LEU* 4.1 1.8 - - - +
53A VAL* 3.0 33.2 - - + +
55A LEU* 5.9 0.7 - - + -
86A ARG* 3.9 14.4 - - + +
87A LYS* 1.3 79.7 - - - +
89A ALA* 1.3 59.8 + - - +
90A CYS* 5.5 0.2 - - - -
112A LEU* 4.1 26.2 - - + -
117A ALA* 3.7 23.1 - - + -
118A GLU 2.9 14.4 + - - +
119A ILE* 3.1 19.6 - - + -
120A VAL* 2.6 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL 3.4 2.4 + - - +
54A LEU* 3.2 18.0 - - + +
55A LEU* 3.2 20.4 + - - +
88A VAL* 1.3 79.3 - - - +
90A CYS* 1.3 67.2 + - - +
119A ILE* 4.7 4.3 - - - -
120A VAL* 4.3 10.5 - - + -
121A GLN* 4.3 19.3 - - + +
140A TRP* 3.6 26.0 - - + -
144A VAL* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.1 13.9 - - - +
88A VAL* 5.5 0.4 - - - -
89A ALA* 1.3 82.0 - - - +
91A PHE* 1.3 63.8 + - - +
105A VAL* 4.0 20.4 - - + +
108A ILE* 3.8 17.5 - - + -
109A GLU* 3.9 21.6 + - + +
112A LEU* 3.6 31.6 - - - -
119A ILE* 6.0 0.9 - - - -
123A GLY* 2.9 28.6 - - - -
124A LEU 2.9 2.9 + - - -
140A TRP* 3.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.9 7.9 - - + -
7A VAL 4.6 1.3 - - - -
8A TYR* 4.7 0.7 - - + -
15A THR* 3.6 28.5 - - + -
18A THR* 3.7 15.5 - - + -
19A ALA* 3.9 19.1 - - + -
22A ILE* 3.6 26.0 - - + -
54A LEU* 4.1 17.5 - - + -
55A LEU 3.0 12.1 + - - +
56A GLY* 2.9 47.6 - - - -
57A CYS 3.1 4.3 + - - +
90A CYS* 1.3 78.0 - - - +
92A GLY* 1.3 61.3 + - - +
105A VAL* 3.9 10.5 - - - +
108A ILE* 5.9 1.0 - - - +
124A LEU* 3.1 34.1 - - + +
140A TRP* 4.2 11.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 4.2 2.7 - - - -
57A CYS 3.4 20.0 - - - -
91A PHE* 1.3 85.0 - - - +
93A CYS* 1.3 65.6 + - - -
102A CYS* 3.4 10.8 - - - -
105A VAL* 4.0 4.4 - - - +
124A LEU* 3.0 6.6 + - - +
126A ILE* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.8 23.3 - - + -
15A THR* 3.4 16.1 + - - +
18A THR* 3.3 26.5 - - - -
57A CYS 4.3 0.2 + - - -
58A SER* 3.4 22.7 - - - -
59A THR* 3.7 4.7 + - - +
92A GLY* 1.3 77.3 - - - -
94A GLY* 1.3 58.9 + - - +
102A CYS* 3.5 5.2 - - - -
126A ILE* 3.5 15.7 - - - +
128A GLY 5.2 1.8 - - - +
130A PRO* 3.9 11.9 - - - -
149A FMN 3.8 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A CYS* 1.3 76.8 - - - +
95A ASP* 1.3 63.0 + - - +
101A PHE* 4.3 2.9 - - - -
102A CYS* 3.6 7.4 - - - -
126A ILE 2.7 17.7 + - - +
128A GLY* 3.2 15.2 + - - +
149A FMN 3.2 34.8 + - - -
----------------------------------------------------------
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