Contacts of the strand formed by residues 102 - 115 (chain O) in PDB entry 5XS0
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 102 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G GLY* 5.7 0.9 - - - -
98O LEU* 3.4 4.8 - - - -
99O ASN 2.8 33.5 + - - +
100O ASN* 4.3 13.5 - - - +
101O GLY* 1.3 83.0 - - - +
103O PHE* 1.3 60.1 + - - +
104O TYR* 3.5 18.3 - - + +
131O GLY* 3.1 33.1 + - - +
132O LEU 3.5 3.4 - - - -
133O LYS* 4.0 18.4 - - + +
3Y C 4.1 4.4 + - - +
4Y C 2.3 35.1 + - - +
5Y C 3.1 28.7 + - - +
7Y C 4.1 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 103 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O VAL* 4.3 11.7 - - + -
97O ASP 3.2 11.4 - - - -
98O LEU* 3.7 36.1 - - + -
101O GLY 4.9 1.3 - - - -
102O LYS* 1.3 72.5 - - - +
104O TYR* 1.3 61.9 + - - +
105O VAL* 4.2 4.3 - - + -
129O SER 3.3 7.1 - - - +
130O GLU 3.8 0.2 - - - -
131O GLY 3.1 20.6 + - - -
132O LEU 2.8 17.6 + - - +
133O LYS* 3.5 21.8 - - - -
135O LYS* 3.5 61.5 - - + -
138O SER* 3.8 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G GLY* 3.3 18.7 + - - -
95O PHE* 3.1 20.5 - - + -
97O ASP* 2.8 41.9 + - + +
99O ASN* 3.8 30.1 + - + +
102O LYS* 3.5 34.1 - - + +
103O PHE* 1.3 75.8 - - - +
105O VAL* 1.3 60.5 + - - +
129O SER 3.3 4.3 - - - +
130O GLU* 3.5 31.0 - - + +
131O GLY* 4.1 2.7 - - - -
2Y C 4.2 4.5 - - - -
3Y C 3.3 43.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136N ALA* 4.1 4.9 - - - +
93O VAL* 4.5 0.2 - - + -
95O PHE* 3.4 14.3 - - - +
96O VAL* 4.0 22.9 - - + -
103O PHE* 4.7 2.0 - - + -
104O TYR* 1.3 81.3 - - - +
106O GLY* 1.3 60.8 + - - +
107O VAL* 3.8 13.2 - - + -
127O GLY 3.8 0.3 - - - +
128O VAL* 3.6 5.7 - - - -
129O SER 2.9 30.6 + - - +
130O GLU* 5.3 0.8 - - - +
135O LYS* 5.6 0.7 - - + +
138O SER* 3.9 27.1 - - - +
139O LEU* 3.8 20.4 - - + +
142O ALA* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136N ALA* 4.3 0.9 - - - -
93O VAL* 3.6 0.5 - - - -
94O ASP* 2.7 30.9 + - - +
95O PHE* 3.2 25.8 + - - +
105O VAL* 1.3 73.4 - - - +
107O VAL* 1.3 61.1 + - - +
126O TYR* 3.5 23.6 - - - -
127O GLY 3.6 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O GLN* 3.7 32.3 - - + +
92O ASN 3.7 6.7 - - - +
93O VAL* 3.7 22.4 - - + -
105O VAL* 3.8 8.5 - - + -
106O GLY* 1.3 78.7 - - - +
108O CYS* 1.3 70.0 + - - +
126O TYR* 3.2 8.0 - - - -
127O GLY 2.7 37.0 + - - -
139O LEU* 4.9 0.2 - - + -
142O ALA* 3.7 28.7 - - + +
143O ARG* 3.9 11.9 - - + -
146O ALA* 3.3 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143N ARG* 3.6 34.3 - - - +
91O GLN* 3.3 2.8 - - - -
92O ASN* 3.0 53.1 + - - +
94O ASP* 4.1 1.1 + - - -
107O VAL* 1.3 78.1 - - - +
109O ALA* 1.3 60.9 + - - +
110O PHE* 3.6 24.7 - - + -
124O VAL* 5.0 2.2 - - + -
125O GLY 3.3 7.9 - - - +
126O TYR* 3.6 19.4 - - + -
146O ALA* 4.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O ILE* 4.8 2.0 - - + -
90O GLN 3.4 7.6 - - - +
91O GLN* 3.9 11.0 - - + +
108O CYS* 1.3 76.3 - - - +
110O PHE* 1.3 64.7 + - - +
111O VAL* 4.0 5.3 + - + -
123O ASP 4.0 0.3 - - - +
124O VAL* 3.4 4.2 - - - +
125O GLY 2.7 35.8 + - - +
146O ALA* 3.7 31.4 - - + +
147O VAL* 3.8 14.1 - - + +
150O GLY* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88N ILE* 4.0 21.8 - - + -
91N GLN* 3.7 42.0 - - + -
143N ARG* 4.2 7.4 - - - -
88O ILE* 3.5 2.8 - - - -
89O THR* 2.6 44.0 + - + -
90O GLN* 2.8 45.4 + - + +
108O CYS* 3.6 26.7 - - + -
109O ALA* 1.3 77.1 - - - +
111O VAL* 1.3 59.6 + - - +
122O GLU* 4.1 6.5 - - - +
123O ASP 3.6 6.1 - - - +
124O VAL* 3.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O HIS* 3.7 31.9 - - + +
87O SER 3.3 11.9 - - - +
88O ILE* 4.7 6.3 - - + -
109O ALA* 4.7 2.5 - - + -
110O PHE* 1.3 79.3 - - - +
112O ARG* 1.3 64.3 + - - +
113O VAL* 4.6 2.0 - - + -
122O GLU* 3.4 3.1 - - - +
123O ASP 3.1 30.7 + - - +
147O VAL* 3.6 36.8 - - + +
150O GLY* 3.7 16.2 - - - -
151O LEU* 3.7 17.5 - - + +
154O ALA* 3.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N SER* 4.9 5.5 - - - -
86O HIS* 3.2 2.1 - - - -
87O SER* 3.0 40.0 + - - +
89O THR* 4.0 15.7 - - - +
110O PHE 4.2 0.8 + - - -
111O VAL* 1.3 73.0 - - - +
113O VAL* 1.3 69.4 + - - +
114O GLN* 3.3 28.5 + - - +
118O GLY 4.8 0.6 + - - -
120O TYR* 3.9 46.9 - - + +
121O HIS 3.6 4.3 - - - +
122O GLU* 4.0 23.3 - - + +
120P TYR* 4.6 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O TRP* 4.4 10.1 - - + -
85O ALA 3.1 12.6 - - - +
86O HIS* 3.8 6.5 - - + -
111O VAL* 4.6 0.9 - - + -
112O ARG* 1.3 71.5 - - - +
114O GLN* 1.3 67.3 + - - +
115O LEU* 5.0 0.4 - - + -
120O TYR* 3.0 7.0 - - - +
121O HIS 2.8 37.7 + - - +
151O LEU* 3.6 30.3 - - + -
154O ALA* 3.7 20.4 - - + -
155O LEU* 3.8 25.8 - - + -
158O PHE* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O PHE* 3.2 26.8 - - + -
27O GLY* 3.9 11.5 - - - -
84O TRP* 3.4 1.9 - - - +
85O ALA 2.7 39.6 + - - +
112O ARG* 3.3 23.2 + - - +
113O VAL* 1.3 75.0 - - - +
115O LEU* 1.3 71.3 + - - +
118O GLY* 3.7 24.9 - - - +
119O SER 3.2 12.1 - - - +
120O TYR* 4.3 5.2 - - + -
120P TYR* 3.3 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81N TYR* 3.8 20.0 - - + -
82N ASN* 4.6 0.2 - - + -
26O PHE* 3.4 13.7 - - - -
31O TYR* 4.0 8.5 - - + +
79O PHE* 3.7 42.2 - - + -
83O GLY 3.4 13.5 - - - +
84O TRP* 3.9 11.0 - - + -
113O VAL* 5.0 0.4 - - + -
114O GLN* 1.3 77.1 + - - +
116O LYS* 1.3 60.2 + - - +
117O ASP* 3.0 21.6 + - - +
118O GLY* 3.0 12.2 + - - -
119O SER* 2.7 20.3 + - - +
158O PHE* 3.5 38.8 - - + -
----------------------------------------------------------
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