Contacts of the strand formed by residues 130 - 138 (chain B) in PDB entry 5YL4
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 LEU 130 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.2 1.4 - - - +
3B GLU 3.5 16.4 - - - +
5B VAL* 3.5 29.4 - - + -
124B SER* 3.5 26.5 - - - +
127B CYS* 4.0 24.3 + - + +
129B CYS* 1.3 71.4 - - - +
131B GLN* 1.3 52.9 + - - +
132B GLY 3.9 14.6 - - - +
133B PHE* 3.7 17.3 - - + -
159B TYR* 4.4 5.8 - - + -
162B ARG* 2.4 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.2 45.7 + - + +
2B ARG* 2.6 31.7 + - - +
3B GLU 2.9 21.0 + - - +
4B ILE* 3.7 25.0 - - + +
46B ARG* 4.3 4.9 - - - +
49B VAL* 4.0 5.7 - - - +
129B CYS 3.4 1.8 + - - -
130B LEU* 1.3 73.2 - - - +
132B GLY* 1.3 57.4 + - - +
162B ARG* 4.4 4.7 + - - -
163B ILE* 3.4 20.3 + - - +
240B LEU* 4.1 10.8 - - - +
249B ASP* 3.2 9.1 - - - +
250B LEU* 3.1 30.8 + - + +
251B ARG* 4.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU 3.9 0.2 + - - -
4B ILE* 3.5 5.8 - - - +
5B VAL 3.1 22.3 + - - -
130B LEU* 3.5 10.0 - - - +
131B GLN* 1.3 84.3 - - - +
133B PHE* 1.3 66.1 + - - -
162B ARG* 4.3 7.9 - - - -
163B ILE 3.1 15.0 - - - -
250B LEU* 4.1 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.6 1.8 - - - -
5B VAL* 3.3 32.8 - - + +
7B ILE* 4.6 9.6 - - + -
120B VAL* 3.7 23.1 - - + -
124B SER* 3.8 9.9 - - - -
130B LEU* 3.7 15.0 - - + -
132B GLY* 1.3 74.8 - - - -
134B GLN* 1.3 63.5 + - - +
155B ILE* 3.4 26.5 - - + -
159B TYR* 3.6 39.5 - + + -
162B ARG* 3.9 14.8 - - + -
163B ILE 2.8 12.7 + - - +
164B MET* 3.6 21.2 - - + -
165B ASN* 3.0 26.3 + - - +
250B LEU* 5.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.8 9.6 - - + +
5B VAL 2.9 7.1 + - - +
6B HIS* 3.2 31.0 + - + +
7B ILE* 3.0 27.9 + - - +
20B PHE* 3.4 13.3 - - - -
50B TYR* 2.6 44.5 + - - -
133B PHE* 1.3 77.0 - - - +
135B LEU* 1.3 60.2 + - - +
165B ASN* 3.2 7.6 - - + +
250B LEU* 6.2 1.3 - - + -
506B 8WR 3.3 52.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.2 38.4 - - + +
9B ALA* 4.9 3.8 - - + -
134B GLN* 1.3 74.8 - - - +
136B THR* 1.3 69.3 + - - +
137B HIS* 3.2 51.8 - - + +
148B GLY* 4.2 24.2 - - - +
151B LEU* 5.0 6.1 - - + -
152B ILE* 4.2 15.0 - - + -
155B ILE* 5.5 0.9 - - + -
164B MET* 5.0 4.9 - - - -
165B ASN 3.0 6.8 + - - +
166B THR* 3.4 14.4 - - + -
167B PHE 2.8 28.6 + - - +
506B 8WR 3.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 3.7 10.1 - - + -
7B ILE 3.1 4.9 + - - -
8B GLN* 3.0 15.1 - - - +
9B ALA 3.0 23.0 + - - -
13B GLY* 2.8 28.3 + - - -
16B ILE* 3.9 12.3 - - + -
17B GLY* 3.9 2.2 - - - -
135B LEU* 1.3 78.1 - - - +
137B HIS* 1.3 63.6 + - - +
167B PHE* 3.6 6.3 - - + -
233B MET* 3.4 33.2 - - + -
506B 8WR 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 3.8 2.9 - - + +
12B CYS* 4.5 3.6 - - - -
13B GLY* 3.6 13.8 - - - -
16B ILE* 4.6 1.4 - - - +
135B LEU* 3.2 25.4 - - + +
136B THR* 1.3 76.0 - - - +
138B SER* 1.3 59.9 + - - +
139B LEU* 3.3 20.0 - - + -
144B GLY* 2.7 38.7 + - - +
148B GLY* 4.6 0.6 - - - -
149B THR* 4.5 9.9 - - + -
152B ILE* 4.6 2.9 - - + -
166B THR* 4.1 6.2 - - - +
167B PHE 3.3 10.6 + - - +
168B SER* 2.7 28.2 + - - -
169B VAL* 3.0 23.6 + - - +
192B LEU* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B CYS* 3.6 16.8 - - - +
13B GLY 4.3 0.6 - - - +
137B HIS* 1.3 76.5 + - - +
139B LEU* 1.3 60.9 + - - +
140B GLY 4.1 0.9 - - - -
141B GLY* 4.1 2.9 + - - -
144B GLY* 3.3 4.9 - - - +
145B SER* 3.1 25.6 + - - -
169B VAL* 3.5 12.6 - - - -
501B GDP 2.7 60.1 + - - -
----------------------------------------------------------
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