Contacts of the strand formed by residues 125 - 130 (chain L) in PDB entry 5A2Q
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 ILE 125 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L SER* 4.4 15.3 - - - +
75L GLY 3.6 7.4 - - - +
76L VAL* 3.9 22.7 - - + -
123L GLY 5.1 2.2 - - - +
124L ASP* 1.3 79.5 - - - +
126L VAL* 1.3 66.6 + - - +
127L THR* 5.0 2.0 - - - +
145L VAL* 3.9 2.4 - - - +
146L THR* 2.6 61.8 + - + +
147L LYS 4.4 5.6 + - - +
148L ALA* 5.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L SER* 3.5 1.7 - - - -
75L GLY 2.9 36.2 + - - +
77L VAL* 3.6 29.8 - - + -
86L ILE* 5.1 1.6 - - + -
88L ILE* 3.6 20.4 - - + -
120L VAL* 6.4 0.2 - - + -
124L ASP* 5.4 0.2 - - - +
125L ILE* 1.3 78.1 - - - +
127L THR* 1.3 64.1 + - - +
128L VAL* 3.9 11.2 + - + +
142L VAL* 3.5 42.0 - - + -
144L LYS 3.8 2.9 - - - +
145L VAL* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L PHE* 4.3 18.8 - - + -
72L ILE* 4.1 14.6 - - + -
73L LEU 3.7 11.4 - - - +
74L SER* 3.6 14.1 - - - -
125L ILE* 4.2 4.4 - - - +
126L VAL* 1.3 72.8 - - - +
128L VAL* 1.3 68.0 + - - +
142L VAL 4.0 0.3 - - - -
143L LEU* 3.0 21.0 + - + -
144L LYS* 3.0 45.5 + - - +
146L THR* 5.1 0.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
72L ILE* 3.2 9.4 - - - +
73L LEU* 2.9 40.5 + - + +
88L ILE* 4.5 15.7 - - + -
109L MET* 4.0 13.9 - - + -
111L VAL* 4.3 9.0 - - + -
126L VAL* 4.0 23.1 - - + +
127L THR* 1.3 79.0 - - - +
129L GLY* 1.3 59.9 + - - +
140L PHE* 3.5 27.1 - - + -
141L ASN 3.3 17.0 - - - +
142L VAL* 4.4 8.3 - - + -
143L LEU* 4.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 129 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L ILE* 4.2 7.4 - - - -
71L ARG 3.7 7.9 - - - -
72L ILE* 4.2 5.4 - - - -
128L VAL* 1.3 75.6 - - - +
130L GLU* 1.3 61.7 + - - -
140L PHE* 3.1 8.0 - - - -
141L ASN* 2.9 33.6 + - - +
143L LEU* 4.0 18.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
1102 U 5.6 0.7 + - - -
1112 A 5.3 1.3 + - - -
3512 G 4.3 17.7 + - - +
3522 U 3.6 36.6 + - - +
68L ILE* 3.7 7.6 - - - +
69L ARG* 2.8 48.1 + - - +
70L GLY* 3.5 15.8 - - - -
71L ARG* 3.1 23.1 + - - +
129L GLY* 1.3 72.8 - - - -
131L CYS* 1.3 79.1 + - - +
139L ARG* 3.8 4.7 - - + +
140L PHE* 3.4 27.6 - - + -
----------------------------------------------------------
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