Contacts of the strand formed by residues 133 - 139 (chain B) in PDB entry 4YCV
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 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B THR* 3.7 26.9 - - + -
110B ILE* 4.0 23.8 - - + -
115B PHE* 4.1 20.2 - - + -
119B TYR* 3.9 24.9 - - + +
131B THR* 3.9 20.0 - - + -
132B ILE* 1.3 82.0 - - - +
134B ASN* 1.3 69.9 + - - +
135B ILE* 4.0 2.5 - - + +
192B ILE 3.5 1.4 - - - +
193B VAL* 3.4 0.5 - - - +
194B GLY 2.9 36.7 + - - +
196B PRO* 4.2 11.9 - - + -
206B ILE* 5.1 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.7 14.1 - - + -
107B GLU* 3.3 25.0 + - - +
108B ARG* 3.3 6.1 - - - +
109B THR* 2.6 44.0 + - - +
110B ILE 3.7 1.8 + - - -
132B ILE* 4.5 3.1 - - - +
133B LEU* 1.3 80.3 + - - +
135B ILE* 1.3 59.4 + - - +
192B ILE 3.3 4.3 - - - -
193B VAL* 3.3 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 4.0 0.9 - - - -
108B ARG* 4.1 0.2 - - - -
110B ILE* 3.5 25.4 - - + +
111B SER* 5.2 0.2 - - - -
112B ILE* 3.6 17.0 - - + +
115B PHE* 3.8 25.4 - - + -
133B LEU* 5.2 2.2 - - + +
134B ASN* 1.3 75.3 - - - +
136B THR* 1.3 73.4 + - - +
154B LEU* 4.5 7.6 - - + -
161B ILE* 3.6 27.4 - - + -
190B VAL 4.1 0.2 - - - +
191B GLY* 3.7 0.7 - - - -
192B ILE* 2.8 50.7 + - + +
206B ILE* 4.2 21.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
351A TYR* 3.1 45.6 - - + -
106B PHE* 3.4 31.9 - - + -
108B ARG* 3.0 35.0 + - + +
112B ILE* 3.9 12.6 - - - +
135B ILE* 1.3 84.7 - - - +
137B GLY* 1.3 59.0 + - - +
154B LEU* 4.3 3.8 - - - -
156B GLY* 5.6 0.5 - - - -
190B VAL 3.5 6.5 - - - -
191B GLY* 4.4 0.2 - - - -
214B LEU* 4.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A TYR* 4.3 7.5 + - - -
136B THR* 1.3 77.9 - - - +
138B ARG* 1.3 60.7 + - - -
154B LEU* 3.5 19.9 - - - +
155B VAL 3.6 9.6 - - - -
156B GLY* 5.4 0.9 - - - -
188B ASP 3.8 0.2 - - - +
189B ILE* 3.3 8.1 - - - +
190B VAL 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 3.7 21.4 + - - +
545A TYR 3.4 19.4 + - - -
546A GLY 3.2 24.4 + - - -
137B GLY* 1.3 73.8 - - - -
139B ILE* 1.3 67.1 + - - +
140B MET* 3.4 14.8 + - - -
153B ASP 3.6 0.2 - - - +
154B LEU* 3.7 2.0 - - - -
155B VAL* 2.9 42.5 + - + +
187B GLY* 2.5 48.2 + - - +
188B ASP 3.3 4.3 - - - +
189B ILE* 3.4 21.4 - - + +
217B CYS* 4.3 3.4 - - - +
221B LEU* 5.0 2.0 - - - +
242B LEU* 3.7 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ARG* 1.3 70.5 - - - +
140B MET* 1.3 61.9 + - - +
141B ARG 3.6 21.5 - - - +
142B VAL* 3.8 19.5 - - + -
152B PHE* 3.8 27.8 - - + -
153B ASP 3.6 3.8 - - - +
154B LEU* 3.7 22.4 - - + -
163B VAL* 5.0 2.7 - - + -
184B ILE* 3.8 22.4 - - + -
186B ARG* 3.6 5.5 - - - +
187B GLY* 2.5 38.2 + - - +
188B ASP* 2.8 21.9 + - + +
190B VAL* 3.9 15.3 - - + -
192B ILE* 5.4 1.3 - - + -
----------------------------------------------------------
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