Contacts of the strand formed by residues 155 - 163 (chain A) in PDB entry 4U86
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 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.7 5.4 - - - -
62A VAL 3.6 9.6 - - - -
64A HIS* 3.9 14.1 + - - -
67A SER* 3.9 8.1 - - - -
151A PHE* 3.7 2.1 - - - +
152A THR* 2.9 33.1 + - - +
153A ASP 3.4 0.2 - - - -
154A SER* 1.4 79.1 - - - +
156A ILE* 1.3 66.2 + - - +
157A HIS* 3.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.5 1.8 - - - +
62A VAL 2.8 34.6 + - - +
64A HIS* 4.2 8.1 - - + +
82A LYS* 3.8 10.5 - - + +
85A ALA* 3.7 11.4 - - + -
86A LEU* 3.5 35.2 - - + +
89A ILE* 3.5 24.7 - - + +
149A PRO* 3.8 26.2 - - + -
150A VAL 3.4 7.6 - - - +
151A PHE* 3.7 32.1 - - + -
155A GLY* 1.3 77.9 - - - -
157A HIS* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 2.9 31.9 + + - -
60A LEU 3.3 6.5 - - - +
61A LEU* 3.6 20.1 - - + +
89A ILE* 4.2 1.3 - - - -
131A GLN* 4.9 3.6 - - - -
134A PHE* 3.5 17.8 - + + -
148A GLY 3.4 4.5 - - - +
149A PRO* 3.5 3.8 - - - +
150A VAL* 2.8 48.6 + - + +
152A THR* 2.8 38.8 + - + +
154A SER* 4.2 7.1 - - - -
155A GLY 3.8 2.2 - - - -
156A ILE* 1.3 78.1 - - - +
158A ILE* 1.3 62.9 + - - +
159A ILE* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 3.0 7.1 - - - +
60A LEU* 2.9 44.3 + - + +
89A ILE* 3.8 28.7 - - + +
92A TYR* 3.9 26.2 - - + -
93A ILE* 3.7 24.9 - - + +
96A ILE* 4.6 4.5 - - + -
103A PHE* 3.8 12.8 - - + -
146A MET* 3.6 35.0 - - + -
147A SER* 3.7 10.1 - - - +
148A GLY 4.3 0.4 - - - -
157A HIS* 1.3 75.5 - - - +
159A ILE* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A CYS* 4.0 13.0 - - + -
58A SER 3.5 9.0 - - - +
103A PHE* 4.7 0.2 - - - -
134A PHE* 3.6 44.2 - - + +
137A ALA* 3.9 26.5 - - + -
138A SER* 3.9 14.6 - - - +
141A LEU* 3.8 16.4 - - + +
146A MET* 3.3 6.1 - - - +
147A SER* 2.8 46.4 + - - +
150A VAL* 4.1 15.5 - - + -
157A HIS* 4.1 6.3 - - + -
158A ILE* 1.3 77.3 - - - +
160A LEU* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A CYS* 3.1 4.4 - - - -
58A SER* 2.8 42.3 + - - +
103A PHE* 4.1 41.2 - - + -
104A GLU* 4.8 10.5 - - - +
144A GLY* 3.7 19.5 - - - +
145A GLU 3.6 18.6 - - - +
146A MET* 4.1 12.1 - - + -
158A ILE 4.3 0.4 + - - -
159A ILE* 1.3 74.8 - - - +
161A ARG* 1.3 60.4 + - - +
162A THR* 3.4 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 3.8 26.4 - - - +
55A VAL* 3.6 12.8 - - + +
56A ARG 3.6 6.1 - - - +
57A CYS* 3.9 8.7 - - - -
138A SER 3.7 12.1 - - - -
139A PHE 4.7 4.9 + - - -
141A LEU* 2.9 45.4 + - + +
142A ARG* 3.7 16.3 - - - +
143A THR* 3.3 22.7 + - - +
144A GLY* 2.8 31.5 + - - -
145A GLU 3.0 7.7 + - - +
160A LEU* 1.3 69.8 - - - +
162A THR* 1.3 62.5 + - - +
163A GLU* 2.9 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 2.8 38.7 + - - +
57A CYS* 4.0 1.9 + - - -
58A SER* 4.1 14.3 + - - +
121A ASP* 4.9 0.5 + - - -
143A THR* 4.0 11.6 - - - +
144A GLY* 4.8 1.6 - - - +
160A LEU* 3.8 31.9 - - + +
161A ARG* 1.3 77.5 - - - +
163A GLU* 1.3 69.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 5.8 0.2 - - - +
54A ARG 4.7 2.8 - - - +
55A VAL* 3.5 5.4 - - - -
56A ARG* 3.0 74.2 + - + +
124A ALA* 5.5 3.6 - - - +
143A THR* 3.7 12.3 + - - -
161A ARG* 2.9 42.0 + - - +
162A THR* 1.3 89.7 - - - +
----------------------------------------------------------
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