Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 4R3O
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 PRO 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 3.4 19.1 + - + +
44A GLY 3.3 24.7 - - - +
45A LYS 4.1 14.6 - - - +
47A CYS 3.3 30.3 - - - +
48A ALA* 4.6 1.3 - - + +
143A ILE* 3.8 18.8 - - + -
147A GLN 4.1 4.6 - - - +
148A GLY* 1.3 87.5 - - - +
150A GLN* 1.3 70.7 + - - +
222A VAL* 4.9 7.9 - - + -
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Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 4.2 14.7 - - - +
48A ALA* 4.3 2.3 - - - +
111A VAL* 4.4 13.8 - - + +
112A ASP* 4.8 6.6 + - - +
141A ILE* 3.2 7.3 - - - +
142A GLY 2.9 39.1 + - - +
144A ASP* 4.0 16.9 - - + +
147A GLN* 3.8 33.0 + - - +
148A GLY 3.8 10.1 - - - +
149A PRO* 1.3 87.6 + - - +
151A VAL* 1.3 64.5 + - - +
152A TYR* 3.3 39.2 + - + -
57B ASP* 5.2 1.8 + - - -
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.0 20.2 - - + +
42A VAL 4.2 5.6 - - - +
43A ARG* 3.9 29.2 + - + +
48A ALA* 4.1 10.1 - - + -
139A ILE* 4.2 9.4 - - + -
140A LEU 3.4 3.4 - - - +
141A ILE* 3.7 15.3 - - + -
150A GLN* 1.3 78.9 - - - +
152A TYR* 1.3 67.0 + - - +
162A GLY* 3.4 4.0 - - - -
163A PHE* 2.9 43.9 + - + +
164A LYS 5.3 0.2 - - - +
165A ALA* 5.5 0.7 - - - -
166A THR* 4.0 20.2 - - - +
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 3.8 27.4 - - + -
112A ASP* 3.9 39.4 + - + +
115A CYS* 3.9 12.8 - - + -
139A ILE* 3.3 8.8 - - - +
140A LEU* 2.9 30.5 + - + -
147A GLN* 5.0 3.6 + - - -
150A GLN* 3.3 37.4 + - + -
151A VAL* 1.3 83.3 - - - +
153A LYS* 1.3 61.5 + - - +
160A TYR* 4.2 17.3 - + - -
161A CYS 3.3 18.6 - - - -
162A GLY* 3.7 19.3 - - - -
163A PHE* 4.7 0.4 - - - -
60B SER* 3.4 23.7 - - - -
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A CYS* 3.5 4.6 - - - -
137A CYS* 3.6 24.5 - - - -
138A MET 3.3 12.8 - - - +
139A ILE* 3.6 28.5 - - + -
152A TYR* 1.3 78.2 - - - +
154A CYS* 1.3 64.0 + - - +
155A ASP* 4.0 13.6 - - - +
160A TYR* 3.1 3.6 - - - -
161A CYS 2.9 31.2 + - - -
163A PHE* 3.7 20.2 - - + -
166A THR* 3.9 21.7 - - + +
167A ALA 3.3 20.5 + - - -
168A ALA* 4.9 0.4 - - - +
172A GLN* 3.6 18.6 - - - +
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Residues in contact with CYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLN* 4.7 2.7 - - - -
115A CYS* 3.7 19.5 - - - +
118A ILE* 3.9 25.6 - - - -
119A ALA* 4.3 13.0 - - + +
122A SER* 6.0 0.4 - - - +
137A CYS* 3.6 22.0 - - - -
138A MET* 3.0 49.7 + - - -
153A LYS* 1.3 73.7 - - - +
155A ASP* 1.3 67.2 + - - +
159A TYR 3.3 9.6 - - - +
160A TYR* 4.1 4.3 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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