Contacts of the strand formed by residues 120 - 129 (chain I) in PDB entry 5XRZ
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 TYR 120 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H PHE* 4.5 4.5 - + - -
85H ALA* 3.1 35.8 + - + +
86H HIS 3.2 23.6 + - - -
87H SER* 3.5 25.6 + - - -
112H ARG* 4.6 6.8 + - - -
114H GLN* 2.8 37.5 + - - +
112I ARG* 3.8 42.0 - - + +
113I VAL 3.1 12.6 - - - +
114I GLN* 4.2 3.8 - - + -
118I GLY 3.3 16.4 - - - +
119I SER* 1.3 77.4 + - - +
121I HIS* 1.3 73.4 + - - +
122I GLU* 5.6 0.2 - - + -
158I PHE* 5.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H TYR 4.1 7.9 - - - -
84H TRP* 3.5 37.8 + + - -
86H HIS* 3.2 35.2 - + + +
112I ARG* 4.4 1.6 - - - -
113I VAL* 2.7 41.0 + - + +
119I SER* 4.7 0.9 - - - -
120I TYR* 1.3 84.8 - - - +
122I GLU* 1.3 57.6 + - - +
154I ALA* 3.7 21.2 - - - +
157I SER* 3.4 30.0 + - - -
158I PHE* 3.2 41.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H HIS* 3.0 30.2 + - - +
87H SER* 3.5 16.4 - - - -
88H ILE* 2.6 60.0 + - + +
147H VAL* 4.8 0.2 - - - +
89I THR* 3.0 38.7 + - - +
110I PHE* 4.3 4.7 - - + +
111I VAL 3.3 17.0 - - - +
112I ARG* 4.1 13.4 - - + -
120I TYR* 5.6 0.2 - - + -
121I HIS* 1.3 74.0 - - - +
123I ASP* 1.3 64.9 + - - +
154I ALA* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H HIS* 4.3 9.5 - - + +
88H ILE* 3.7 9.2 - - - -
147H VAL* 3.6 18.6 - - - +
148H THR* 5.1 0.5 + - - -
151H LEU* 5.7 1.7 - - - +
110I PHE* 3.7 1.6 - - - -
111I VAL* 3.1 31.6 + - - +
122I GLU* 1.3 75.3 - - - +
124I VAL* 1.3 78.8 + - - +
150I GLY 4.1 4.1 - - - +
153I ARG* 2.8 71.4 + - + +
154I ALA* 3.9 3.5 - - - +
157I SER* 4.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ILE* 3.7 1.8 - - + -
91H GLN* 3.8 11.7 - - - +
143H ARG* 4.5 10.5 - - + +
144H LYS* 4.9 11.7 - - + -
147H VAL* 3.4 31.4 - - + -
108I CYS* 4.4 9.0 - - + -
109I ALA 3.3 13.7 - - - +
110I PHE* 3.5 34.8 - - + +
123I ASP* 1.3 85.8 + - - +
125I GLY* 1.3 73.5 + - - +
126I TYR* 5.5 1.3 - - + -
150I GLY* 3.5 3.3 - - - -
153I ARG* 3.2 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H LYS* 4.4 3.1 - - - -
108I CYS* 3.3 4.9 - - - +
109I ALA 2.7 34.6 + - - -
124I VAL* 1.3 78.2 - - - +
126I TYR* 1.3 59.6 + - - -
146I ALA* 3.5 8.0 - - - +
149I ASP* 3.7 8.1 - - - -
150I GLY* 3.3 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H ALA* 3.7 14.8 - - - -
139H LEU* 3.2 36.7 - - + +
140H GLU* 3.7 41.6 - - + +
143H ARG* 4.0 11.7 - - + -
144H LYS* 4.1 4.2 - - + +
94I ASP* 2.6 34.5 + - - +
95I PHE* 4.0 0.7 - - - -
106I GLY* 3.8 10.0 - - - -
107I VAL 3.3 24.2 - - - -
108I CYS* 3.6 19.1 - - + -
124I VAL* 5.5 1.1 - - + -
125I GLY* 1.3 74.9 - - - -
127I GLY* 1.3 70.1 + - - +
128I VAL* 3.8 12.1 - - + -
145I GLU* 3.6 15.5 - - - +
146I ALA* 3.4 11.4 - - - -
149I ASP* 3.7 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I VAL 3.9 0.5 - - - +
106I GLY* 3.8 1.6 - - - -
107I VAL 2.7 36.1 + - - +
126I TYR* 1.3 79.3 - - - +
128I VAL* 1.3 62.5 + - - +
142I ALA* 3.3 26.9 - - - +
145I GLU* 3.7 8.7 - - - -
146I ALA* 3.5 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H ALA* 3.6 30.1 - - + +
137H LEU* 4.7 7.4 - - + -
140H GLU* 4.1 17.7 - - - +
105I VAL 3.6 3.8 - - - +
126I TYR* 3.8 12.1 - - + -
127I GLY* 1.3 80.4 - - - +
129I SER* 1.3 61.8 + - - +
130I GLU* 3.5 30.7 - - + +
141I LYS* 3.2 23.9 + - - -
142I ALA* 4.1 3.0 - - - +
145I GLU* 3.3 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I PHE 3.0 7.6 - - - +
105I VAL* 2.9 33.9 + - - +
128I VAL* 1.3 74.8 - - - +
130I GLU* 1.3 60.2 + - - +
131I GLY 4.8 0.2 + - - -
132I LEU* 3.8 10.6 + - - +
138I SER* 3.1 47.9 + - - -
141I LYS* 3.7 23.1 + - - +
142I ALA* 4.5 2.8 - - - +
----------------------------------------------------------
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