Contacts of the strand formed by residues 143 - 147 (chain W) in PDB entry 2YGD
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 143 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78W ASN 3.6 0.7 - - - -
79W LEU* 2.7 57.3 + - + +
89W LEU* 5.1 2.5 - - + -
91W VAL* 3.9 23.1 - - + -
100W VAL* 3.5 22.4 - - + -
135W SER* 3.7 10.1 - - - +
136W SER 3.3 31.0 - - - +
137W LEU* 3.5 13.2 - - + +
141W GLY 3.3 6.7 + - - +
142W VAL* 1.3 73.8 - - - +
144W THR* 1.3 61.1 + - - +
145W VAL* 3.5 31.4 - - + -
160X PRO 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61W PHE 5.1 1.0 + - - -
62W ASP* 4.9 4.9 + - - +
65W LEU 4.1 11.8 + - - +
76W SER* 4.0 17.3 - - - +
77W VAL 3.3 11.2 - - - +
78W ASN* 3.2 21.3 + - - +
134W THR 3.7 1.4 - - - +
135W SER* 3.6 0.3 - - - -
136W SER* 2.7 47.1 + - - -
142W VAL* 4.3 2.3 - - - +
143W LEU* 1.3 72.9 - - - +
145W VAL* 1.3 70.4 + - - +
146W ASN* 3.9 0.8 - - + +
163X ARG* 3.7 34.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75W PHE* 5.7 0.8 - - + -
76W SER* 3.2 4.7 - - - -
77W VAL* 2.8 65.0 + - + +
79W LEU* 4.1 6.5 - - + -
98W ILE* 3.5 25.1 - - + -
128W VAL* 4.7 7.2 - - + -
133W ILE* 3.6 25.1 - - + +
134W THR 3.3 4.0 - - - +
135W SER* 3.2 23.8 - - - +
143W LEU* 3.5 18.3 - - + +
144W THR* 1.3 71.2 - - - +
146W ASN* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 146 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74W ARG* 5.5 4.0 - - + +
75W PHE 3.3 9.2 - - - -
76W SER* 3.4 17.0 - - - +
133W ILE* 3.3 9.1 - - - -
134W THR* 2.8 53.6 + - - +
136W SER* 3.4 22.2 + - - -
144W THR* 3.9 3.3 - - + +
145W VAL* 1.3 71.8 - - - +
147W GLY* 1.3 60.4 + - - +
131X LEU* 4.3 4.3 - - - +
163X ARG* 3.6 22.5 - - + +
164X GLU* 4.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73W ASP* 5.0 1.3 - - - -
74W ARG* 3.4 14.6 - - - +
75W PHE* 2.8 30.4 + - - +
132W THR 3.9 4.9 - - - -
133W ILE* 3.5 2.3 - - - +
134W THR* 4.6 1.3 - - - -
146W ASN* 1.3 81.4 - - - +
148W PRO* 1.3 74.7 - - - +
134X THR* 6.2 0.2 - - - -
----------------------------------------------------------
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