Contacts of the strand formed by residues 120 - 132 (chain L) 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 TYR 120 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L ARG* 3.9 45.3 - - + +
113L VAL 3.1 12.6 - - - +
114L GLN* 4.4 2.0 - - - -
118L GLY 3.3 21.5 - - - +
119L SER* 1.3 77.9 + - - +
121L HIS* 1.3 74.3 + - - +
158L PHE* 4.8 1.1 - - - -
26V PHE* 4.2 6.1 - + - -
85V ALA* 3.1 40.4 - - + +
86V HIS* 3.3 27.4 - - - -
87V SER* 3.8 17.4 + - - -
112V ARG* 5.0 5.4 + - - -
114V GLN* 2.9 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L ARG* 4.5 1.3 - - - -
113L VAL* 2.9 30.0 + - - +
119L SER* 4.4 0.9 - - - -
120L TYR* 1.3 79.3 + - - +
122L GLU* 1.3 60.5 + - - +
154L ALA* 3.6 25.4 - - - +
157L SER* 3.5 21.0 - - - -
158L PHE* 3.2 42.2 - + + -
81V TYR 4.0 7.0 - - - -
84V TRP* 3.2 50.6 + + - -
86V HIS* 3.0 37.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L THR* 3.0 38.9 + - - +
110L PHE* 4.0 7.0 - - + +
111L VAL 3.3 15.0 - - - +
112L ARG* 4.0 18.3 - - + +
120L TYR* 5.6 0.2 - - + -
121L HIS* 1.3 75.4 - - - +
123L ASP* 1.3 66.0 + - - +
86V HIS* 2.8 31.4 + - - +
87V SER* 3.3 21.6 - - - -
88V ILE* 2.9 47.9 + - + +
147V VAL* 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L PHE* 3.5 4.3 - - - +
111L VAL* 3.0 31.8 + - - +
122L GLU* 1.3 75.3 - - - +
124L VAL* 1.3 73.9 + - - +
150L GLY 4.6 2.2 - - - +
153L ARG* 3.3 46.5 + - + +
154L ALA* 3.8 24.4 - - + +
157L SER* 4.6 3.5 + - - -
86V HIS* 4.3 7.7 + - - +
88V ILE* 3.6 11.7 - - - +
147V VAL* 3.6 17.9 - - - +
148V THR* 5.4 1.7 + - - -
151V LEU* 5.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L CYS* 4.3 9.6 - - + -
109L ALA 3.3 10.8 - - - +
110L PHE* 4.1 24.2 - - + +
123L ASP* 1.3 85.2 + - - +
125L GLY* 1.3 72.0 + - - +
126L TYR* 5.5 0.9 - - + -
150L GLY* 3.9 2.9 - - - -
153L ARG* 2.8 29.1 + - - -
88V ILE* 3.9 0.8 - - - +
91V GLN* 4.2 7.2 - - - +
143V ARG* 4.0 7.4 - - + +
144V LYS* 3.9 27.8 - - + +
147V VAL* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L CYS* 3.3 4.5 - - - +
109L ALA 2.7 31.8 + - - +
124L VAL* 1.3 78.9 - - - +
126L TYR* 1.3 60.3 + - - -
146L ALA* 3.4 9.0 - - - -
149L ASP* 3.4 6.5 - - - -
150L GLY* 3.3 27.1 - - - -
144V LYS* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L ASP* 2.6 36.1 + - - +
95L PHE* 3.9 0.3 - - - -
106L GLY* 3.5 13.2 - - - -
107L VAL 3.2 26.5 - - - -
108L CYS* 3.6 15.3 - - + -
124L VAL* 5.5 0.9 - - + -
125L GLY* 1.3 73.5 - - - -
127L GLY* 1.3 69.6 + - - +
128L VAL* 3.8 9.2 - - + -
145L GLU* 3.5 12.5 - - - +
146L ALA* 3.4 11.2 - - - -
149L ASP* 3.2 15.4 + - - +
136V ALA* 3.3 19.1 - - - -
139V LEU* 3.2 24.2 - - + +
140V GLU* 3.5 42.5 - - + +
143V ARG* 3.8 13.7 - - + -
144V LYS* 4.2 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L GLY* 3.6 5.0 - - - -
107L VAL 2.7 36.0 + - - -
126L TYR* 1.3 76.2 - - - +
128L VAL* 1.3 63.6 + - - +
142L ALA* 3.3 30.5 - - - +
145L GLU* 3.7 7.6 - - - -
146L ALA* 3.6 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L VAL 3.4 3.6 - - - -
126L TYR* 3.8 19.5 - - + -
127L GLY* 1.3 78.5 - - - +
129L SER* 1.3 64.8 + - - +
130L GLU* 3.4 32.8 - - + +
141L LYS* 3.4 21.5 + - - +
142L ALA* 4.2 3.0 - - - +
145L GLU* 3.5 19.4 + - - +
136V ALA* 3.5 21.5 - - + -
137V LEU* 4.1 16.6 - - + -
140V GLU* 4.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L PHE 3.2 7.2 - - - +
105L VAL* 2.8 37.7 + - - +
128L VAL* 1.3 76.9 - - - +
130L GLU* 1.3 61.1 + - - +
132L LEU* 3.7 14.9 - - - +
138L SER* 3.2 49.2 + - - -
141L LYS* 4.1 15.0 - - - +
142L ALA* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L PHE 3.5 2.7 - - - -
104L TYR* 3.7 31.5 - - + -
105L VAL 5.2 0.2 - - - +
128L VAL* 3.4 26.1 - - + +
129L SER* 1.3 76.8 + - - +
131L GLY* 1.3 59.3 + - - +
132L LEU* 3.5 6.6 + - - +
141L LYS* 5.5 0.6 - - - +
134V SER* 2.6 36.8 + - - -
135V LYS 5.5 0.2 + - - -
136V ALA* 4.6 4.5 - - + -
137V LEU* 3.8 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L LYS* 3.3 38.5 - - - +
103L PHE 3.0 9.3 + - - -
104L TYR* 4.3 7.8 - - - -
130L GLU* 1.3 71.7 - - - +
132L LEU* 1.3 65.5 + - - +
133L LYS* 3.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L PHE* 2.7 36.6 + - - +
129L SER* 3.7 18.4 - - - +
130L GLU 3.5 4.3 - - - +
131L GLY* 1.3 78.4 - - - +
133L LYS* 1.3 61.6 + - - +
134L SER* 3.4 5.8 - - - +
137L LEU* 4.1 33.4 - - + +
138L SER* 3.4 20.4 - - - +
141L LYS* 5.0 11.0 - - + +
----------------------------------------------------------
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