Contacts of the helix formed by residues 144 - 155 (chain A) in PDB entry 4RTP
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.4 42.6 - - + +
81A PHE* 4.5 4.7 - - + -
112A LEU* 4.3 13.9 - - + -
116A ARG* 4.3 10.3 - - - +
142A TYR* 3.2 22.2 - - + +
143A PHE* 1.3 89.6 - - + +
145A GLU* 1.3 58.6 + - - +
146A ALA 3.4 2.5 - - - -
147A GLU* 3.3 18.6 + - + +
148A LEU* 2.9 30.8 + - + +
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Residues in contact with GLU 145 (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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74A VAL* 4.1 7.2 - - + -
78A ARG* 3.0 42.6 + - - -
142A TYR* 4.5 0.6 + - - -
143A PHE* 2.8 28.8 + - + +
144A PRO* 1.3 72.0 - - - +
146A ALA* 1.3 65.1 + - - +
147A GLU* 4.0 0.2 + - - -
148A LEU* 3.2 7.6 + - - +
149A TYR* 3.1 51.9 + - + -
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Residues in contact with ALA 146 (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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142A TYR* 4.8 4.8 + - - +
144A PRO 3.4 0.4 - - - -
145A GLU* 1.3 78.2 - - - +
147A GLU* 1.3 66.0 + - - +
149A TYR* 3.3 7.4 + - - +
150A HIS* 3.0 29.9 + - - +
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Residues in contact with GLU 147 (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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5A ARG* 3.3 38.5 - - + +
6A ALA 4.2 6.7 - - - +
7A PHE* 3.7 24.4 + - + -
43A LEU* 5.6 1.6 - - - +
142A TYR* 3.0 37.7 + - - -
144A PRO* 3.3 12.6 - - + +
145A GLU 3.3 0.2 - - - -
146A ALA* 1.3 79.4 + - - +
148A LEU* 1.3 57.7 + - - +
150A HIS* 4.0 6.9 + - - +
151A PHE* 3.1 28.1 + - - +
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Residues in contact with LEU 148 (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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7A PHE* 3.5 36.6 - - + -
66A VAL* 4.0 18.1 - - + +
70A THR* 5.3 1.8 - - + -
73A TYR* 4.1 20.9 - - + -
74A VAL* 4.2 21.8 - - + -
112A LEU* 3.9 20.0 - - + -
143A PHE* 4.1 20.9 - - + -
144A PRO* 2.9 23.3 + - + +
145A GLU* 3.4 8.7 - - - +
146A ALA 3.1 0.2 - - - -
147A GLU* 1.3 75.1 - - - +
149A TYR* 1.3 60.5 + - - +
151A PHE* 3.2 5.9 + - - +
152A ALA* 3.0 28.3 + - - +
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Residues in contact with TYR 149 (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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70A THR* 3.6 22.0 - - + -
71A ASP* 3.0 30.4 + - - -
74A VAL* 3.6 25.8 - - + +
78A ARG* 5.1 1.2 + - - -
145A GLU* 3.1 51.4 + - + +
146A ALA* 3.9 5.8 - - - +
148A LEU* 1.3 79.3 - - - +
150A HIS* 1.3 62.3 + - - +
152A ALA* 3.4 5.3 + - + +
153A GLU* 3.1 35.6 + - + +
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Residues in contact with HIS 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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4A ASN* 3.3 44.5 + - + +
5A ARG 5.6 1.8 + - - -
43A LEU* 3.9 15.5 - - + +
146A ALA 3.0 17.5 + - - +
147A GLU* 4.0 7.2 + - - +
149A TYR* 1.3 73.2 - - - +
151A PHE* 1.3 66.0 + - - +
153A GLU* 3.6 11.5 + - + +
154A LYS* 3.2 50.7 + - + +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.5 24.0 - + + -
38A ALA 4.7 7.2 - - - -
39A GLY* 5.6 0.7 - - - -
42A PHE* 3.8 18.3 - + - -
43A LEU* 3.8 28.3 - - + -
63A TYR* 3.3 59.9 - + + -
66A VAL* 3.9 12.1 - - + -
67A LYS 5.5 0.2 - - - -
147A GLU 3.1 19.7 + - - +
148A LEU 3.5 4.5 - - - +
150A HIS* 1.3 78.4 + - - +
152A ALA* 1.3 58.3 + - - +
154A LYS* 3.3 2.1 + - - +
155A ALA* 2.8 34.7 + - + +
160A PHE* 3.7 27.1 - + - -
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Residues in contact with ALA 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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66A VAL* 3.8 10.5 - - + +
67A LYS* 4.7 6.0 - - - +
70A THR* 3.2 37.9 - - + +
148A LEU 3.0 15.5 + - - +
149A TYR* 3.7 4.9 - - + +
150A HIS 3.3 0.4 - - - -
151A PHE* 1.3 81.1 - - - +
153A GLU* 1.3 60.9 + - + +
155A ALA* 3.3 15.2 + - - +
156A GLN* 3.4 19.1 + - - +
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A TYR* 3.1 24.1 + - + +
150A HIS* 3.9 12.1 - - + +
151A PHE 3.3 0.2 - - - -
152A ALA* 1.3 78.6 - - + +
154A LYS* 1.3 61.7 + - + +
156A GLN* 3.4 33.3 + - - +
157A ASN* 4.5 4.3 - - - +
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Residues in contact with LYS 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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4A ASN* 5.4 0.2 - - - +
42A PHE* 2.8 53.6 + - + +
43A LEU* 4.2 10.2 + - + +
45A THR 2.6 30.1 + - - -
46A ASP* 4.6 4.2 + - - +
50A TYR* 3.4 13.9 + - - -
150A HIS* 3.2 44.9 + - + +
151A PHE 3.9 1.6 - - - +
153A GLU* 1.3 74.5 - - + +
155A ALA* 1.3 60.3 + - - +
156A GLN 3.1 6.6 + - - -
157A ASN* 3.3 19.8 + - - +
158A ALA 4.1 0.2 + - - -
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Residues in contact with ALA 155 (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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42A PHE* 4.0 7.9 - - + -
67A LYS* 2.9 39.6 + - + -
151A PHE* 2.8 22.8 + - + +
152A ALA* 3.6 9.4 - - - +
153A GLU 3.2 0.4 - - - -
154A LYS* 1.3 73.8 - - - +
156A GLN* 1.3 55.3 + - - +
157A ASN 3.0 6.1 - - - -
158A ALA* 3.0 15.9 + - - +
160A PHE* 3.8 25.4 - - + -
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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