Contacts of the helix formed by residues 140 - 150 (chain B) in PDB entry 5ITY
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 GLU 140 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 6.3 0.9 - - - +
52B ARG* 2.9 30.5 + - - -
135B PRO* 3.3 13.9 - - + +
136B CYS* 2.7 41.6 + - + +
139B GLN* 1.3 88.3 - - + +
141B TYR* 1.3 64.2 + - - +
142B GLN 3.3 2.0 - - - -
143B GLN* 3.1 14.2 + - + +
144B PHE* 2.8 22.5 + - - +
501B GOL 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A HIS* 6.2 2.0 - + - -
139A GLN* 4.0 16.2 - - - +
136B CYS 3.8 0.6 + - - -
137B VAL 4.2 5.6 + - - -
140B GLU* 1.3 75.8 - - - +
142B GLN* 1.3 62.7 + - + +
144B PHE* 3.1 13.9 + + - +
145B ARG* 2.7 76.7 + - + +
226B LEU 3.3 21.8 - - - -
227B GLU* 3.4 21.9 - - + +
230B HIS* 3.4 40.8 - + + +
501B GOL 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A HIS* 4.1 16.9 + - + -
11A SER* 2.8 26.9 + - - -
12A GLN* 4.4 8.7 - - - +
15A ASN* 4.3 10.5 + - - +
49A ALA 3.8 14.3 + - - +
50A SER* 3.3 12.7 - - - +
51A ALA* 2.8 25.1 + - - +
139A GLN* 3.0 30.4 - - - +
140B GLU 3.3 0.6 - - - -
141B TYR* 1.3 87.8 - - + +
143B GLN* 1.3 63.7 + - - +
145B ARG* 3.5 7.3 - - - +
146B GLU* 3.0 26.3 + - - +
501B GOL 5.0 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 2.8 33.9 + - - -
49A ALA* 3.2 31.2 + - - +
50A SER* 3.8 11.5 + - - +
57A ARG* 6.3 1.3 - - - +
59A ILE* 3.7 28.0 - - + +
135B PRO* 3.9 17.9 - - + -
140B GLU* 3.1 17.5 + - + +
142B GLN* 1.3 77.3 - - - +
144B PHE* 1.3 65.5 + - - +
146B GLU* 4.1 3.3 - - - +
147B ASN* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PRO* 3.7 29.5 - - + +
136B CYS 4.3 2.9 - - - +
137B VAL* 3.7 23.6 - - + -
140B GLU 2.8 18.1 + - - +
141B TYR* 3.5 19.3 - + - -
143B GLN* 1.3 77.8 - - - +
145B ARG* 1.3 78.9 + - - +
147B ASN* 3.1 1.9 + - - +
148B VAL* 3.0 27.3 + - + +
170B PHE 3.0 28.9 - - - -
171B PHE* 3.4 13.9 - + - -
226B LEU* 3.5 39.9 - - + -
229B CYS* 3.6 24.5 - - + -
230B HIS 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 2.7 65.6 + - + +
142B GLN* 3.5 8.1 - - - +
144B PHE* 1.3 83.4 - - - +
146B GLU* 1.3 64.1 + - + +
148B VAL* 3.2 4.9 + - - +
149B LEU* 3.1 35.9 + - + +
201B LEU 4.4 14.6 + - - -
224B ASP* 3.3 34.9 + - - -
226B LEU* 3.5 37.2 - - + +
227B GLU 3.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 3.1 43.2 - - + +
19A ARG* 2.7 47.1 + - - +
48A SER* 4.6 6.5 - - - -
142B GLN 3.0 14.7 + - - +
143B GLN* 4.1 4.5 - - - +
145B ARG* 1.3 77.2 - - + +
147B ASN* 1.3 62.2 + - - +
149B LEU* 3.2 4.5 + - - +
150B ARG* 2.8 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLY* 4.6 1.2 - - - -
135B PRO* 4.1 20.5 - - + +
143B GLN* 2.8 19.1 + - - +
144B PHE 3.6 4.0 + - - +
146B GLU* 1.3 74.9 - - - +
148B VAL* 1.3 61.8 + - - +
150B ARG* 4.7 2.5 - - - +
151B ASN* 2.6 40.9 + - - +
169B ARG 3.6 12.5 + - - -
170B PHE* 3.5 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 3.0 26.4 + - + +
145B ARG 3.5 7.6 - - - +
147B ASN* 1.3 75.4 - - - +
149B LEU* 1.3 69.8 + - + +
151B ASN 2.9 14.7 + - - -
152B LEU* 3.2 28.8 + - + +
157B PHE* 4.2 6.6 - - + -
170B PHE* 3.5 37.2 - - + +
171B PHE* 4.0 12.3 - - + -
198B LEU* 4.2 11.4 - - + -
226B LEU* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 3.6 47.6 - - - +
145B ARG* 3.1 38.1 + - + +
146B GLU* 4.1 4.3 - - - +
148B VAL* 1.3 82.8 - - + +
150B ARG* 1.3 59.8 + - - +
151B ASN 3.2 0.7 + - - -
152B LEU* 3.9 21.9 + - + +
198B LEU* 5.1 5.6 - - + +
200B ALA 4.7 3.1 - - - +
201B LEU* 3.7 44.6 - - + +
226B LEU* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 3.0 34.2 + - - +
18A CYS* 3.6 18.5 + - - +
19A ARG* 3.7 24.2 - - - +
46A ARG* 3.8 40.9 + - - +
47A ILE 2.5 37.1 + - - +
48A SER* 3.9 6.8 - - - -
146B GLU* 2.8 44.5 + - - +
147B ASN* 4.7 1.6 - - - +
149B LEU* 1.3 80.5 - - - +
151B ASN* 1.3 72.1 + - - +
152B LEU 3.7 0.4 - - - -
----------------------------------------------------------
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