Contacts of the strand formed by residues 130 - 140 (chain L) in PDB entry 3LS5
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 GLY 130 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125L GLN* 3.1 32.7 + - - +
126L LEU* 3.4 14.7 - - - +
128L SER* 3.6 3.0 + - - -
129L GLY* 1.3 80.6 - - - +
131L ALA* 1.3 62.2 + - - +
181L THR* 5.8 1.6 - - - -
182L LEU 3.7 7.0 - - - -
183L THR* 4.6 0.4 - - - -
184L LYS 4.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L PRO* 3.8 12.6 - - + -
125L GLN* 3.7 4.0 - - - +
126L LEU* 3.9 6.7 - - + -
130L GLY* 1.3 74.4 - - - +
132L SER* 1.3 63.5 + - - +
133L VAL* 5.0 1.1 - - - +
180L LEU 3.8 1.2 - - - +
181L THR* 3.5 1.0 - - - +
182L LEU* 2.8 44.9 + - + +
183L THR 3.9 3.4 - - - +
187L TYR* 3.4 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LEU* 5.6 1.4 - - - +
145H LEU* 3.5 25.4 - - - +
147H LYS* 3.9 4.3 - - - -
119L PHE 4.3 0.2 - - - +
120L PRO 4.0 1.9 - - - +
121L PRO* 3.5 22.9 - - - +
125L GLN* 2.9 34.1 + - - +
131L ALA* 1.3 72.6 - - - +
133L VAL* 1.3 63.1 + - - +
134L VAL* 4.2 3.0 + - - +
179L THR* 3.9 6.7 - - - +
180L LEU 3.2 4.5 - - - -
181L THR* 2.8 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L ILE* 4.0 4.5 - - + -
119L PHE 3.4 15.9 - - - +
121L PRO* 4.1 18.4 - - + -
131L ALA 5.0 2.2 - - - +
132L SER* 1.3 79.0 - - - +
134L VAL* 1.3 60.7 + - - +
149L TRP* 3.5 31.6 - - + -
179L THR* 3.4 2.4 - - - -
180L LEU* 2.7 44.4 + - + +
182L LEU* 5.6 2.2 - - + -
187L TYR* 4.6 4.7 - - + -
193L TYR* 4.3 18.2 - - + -
210L PHE* 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LEU* 3.9 33.0 - - + -
145H LEU* 4.2 15.3 - - + -
182H SER* 5.1 1.1 - - - -
118L ILE* 3.3 4.9 - - - +
119L PHE* 2.8 39.1 + - + -
132L SER 4.2 0.9 + - - +
133L VAL* 1.3 77.6 - - - +
135L CYS* 1.3 66.8 + - - +
136L PHE* 3.9 36.1 - - + -
149L TRP* 4.1 2.5 - - - -
177L SER* 4.2 6.3 - - - +
178L SER 3.6 7.0 - - - +
179L THR* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 135 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L VAL* 3.6 21.5 - - - -
117L SER 3.2 5.8 - - - -
118L ILE* 5.0 0.4 - - - -
134L VAL* 1.3 75.6 - - - +
136L PHE* 1.3 62.9 + - - +
137L LEU* 3.7 15.0 - - - +
147L VAL* 5.2 0.9 - - - -
149L TRP* 3.7 17.0 - - + -
177L SER* 3.5 4.3 + - - -
178L SER* 2.9 36.8 + - - +
195L CYS* 2.1 45.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LEU* 3.8 31.0 - - + -
141H THR* 4.4 2.5 - - + -
142H LEU 4.2 5.2 - - - -
143H GLY* 4.2 1.1 - - - -
170H PHE* 3.5 30.7 - + - -
182H SER* 3.6 9.6 - - - -
183H SER 3.8 9.9 - - - -
184H SER* 3.5 27.6 - - - -
115L THR 3.3 2.0 - - - +
116L VAL* 3.3 5.4 - - - +
117L SER* 2.9 37.4 + - - +
119L PHE* 3.4 29.2 - + - -
134L VAL* 3.9 6.1 - - + -
135L CYS* 1.3 73.6 - - - +
137L LEU* 1.3 62.6 + - - +
138L ASN* 3.9 17.0 - - - +
176L MET 3.5 1.3 - - - -
177L SER* 3.4 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L PRO* 4.3 9.4 - - + -
115L THR 3.6 5.4 - - - -
116L VAL* 4.0 11.2 - - + -
135L CYS* 3.7 27.6 - - + +
136L PHE* 1.3 79.4 - - - +
138L ASN* 1.3 58.4 + - - +
140L PHE* 3.2 19.8 - - + -
145L ILE* 4.0 7.6 - - + -
147L VAL* 3.7 28.3 - - + -
175L SER* 3.3 0.2 - - - -
176L MET* 2.8 48.7 + - + +
178L SER* 4.6 3.4 - - - -
195L CYS* 5.7 0.4 - - - -
197L ALA* 3.3 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H THR* 4.5 10.3 + - - +
168H HIS* 3.8 13.5 - - + -
170H PHE* 3.6 12.8 - - - -
184H SER* 3.1 24.7 + - - -
186H THR* 4.9 5.3 + - - -
114L PRO* 3.4 1.6 - - - +
115L THR* 2.9 42.5 + - + +
136L PHE* 3.9 15.3 - - - +
137L LEU* 1.3 79.1 + - - +
139L ASN* 1.3 82.6 + - - +
140L PHE* 3.4 3.0 + - - -
175L SER* 3.3 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H HIS* 2.7 38.1 + - - -
112L ALA* 3.6 17.2 - - - +
113L ALA 3.7 5.5 - - - +
115L THR* 5.5 4.6 + - - +
138L ASN* 1.3 80.5 - - - +
140L PHE* 1.3 58.9 + - - +
171L ASP* 4.4 10.5 + - - +
173L THR* 3.3 29.3 + - + +
174L TYR 3.2 2.1 + - - -
175L SER* 2.9 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L ALA* 3.3 13.5 - - - +
114L PRO* 3.6 30.1 - - + -
137L LEU 3.2 26.5 - - - -
139L ASN* 1.3 76.4 - - - +
141L TYR* 1.3 64.5 + - - +
142L PRO 3.2 20.4 - - - -
143L LYS 3.2 26.2 - - - -
145L ILE* 3.5 31.2 - - + -
164L TRP* 5.0 4.0 - + - -
173L THR* 3.5 2.2 - - - -
174L TYR* 2.7 65.4 + - + -
175L SER* 3.7 7.2 - - - -
176L MET* 3.9 9.2 - - + -
199L HIS* 3.7 9.2 - + - +
----------------------------------------------------------
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