Contacts of the helix formed by residues 141 - 150 (chain A) in PDB entry 4F5G
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A SER 3.3 7.4 - - - +
140A TRP* 1.3 98.7 - - + +
142A ASN* 1.3 68.7 + - - +
143A HIS 3.4 0.7 + - - -
144A LYS* 4.0 12.3 + - - +
145A ALA* 4.6 2.3 + - - +
193A ASN* 5.4 3.1 - - - +
194A PRO* 6.2 0.7 - - + -
384A ARG* 5.7 8.3 - - - +
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Residues in contact with ASN 142 (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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140A TRP* 3.1 40.7 + - + +
141A PRO* 1.3 84.5 - - - +
143A HIS* 1.3 65.4 + - - +
144A LYS 3.2 1.3 - - - -
145A ALA* 3.3 8.4 + - + +
146A ILE* 3.1 29.1 + - + +
290B ARG* 3.9 35.0 + - - +
294B SER* 4.1 17.0 + - - -
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Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.7 14.3 - - + +
135A VAL* 4.1 19.3 - - + +
139A SER* 3.0 27.3 + - - +
140A TRP* 3.2 37.2 + + + +
142A ASN* 1.3 77.8 - - - +
144A LYS* 1.3 64.7 + - - +
146A ILE* 3.2 2.6 + - - +
147A PHE* 3.0 36.4 + + + -
154A VAL* 4.9 0.7 - - - -
186A LEU* 3.6 37.8 - - + +
188A HIS* 3.8 5.2 - + - -
221A ASP* 2.6 29.4 + - - -
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Residues in contact with LYS 144 (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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135A VAL* 6.0 0.6 - - + +
140A TRP 4.7 0.6 + - - -
141A PRO 4.0 8.5 + - - +
142A ASN 3.2 1.0 - - - -
143A HIS* 1.3 79.7 - - - +
145A ALA* 1.3 56.5 + - - +
148A ASN* 2.9 61.0 + - - +
154A VAL* 3.9 32.2 + - + +
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Residues in contact with ALA 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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141A PRO 4.6 1.9 + - - +
142A ASN* 3.3 13.7 + - - +
143A HIS 3.3 0.4 - - - -
144A LYS* 1.3 78.6 - - - +
146A ILE* 1.3 58.5 + - - +
148A ASN* 3.8 5.5 - - - +
149A SER* 2.9 30.7 + - - -
287B ALA 5.9 0.2 - - - +
290B ARG* 5.0 12.1 - - + +
291B ALA* 3.5 19.9 - - + +
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Residues in contact with ILE 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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114A SER* 4.1 13.9 - - - +
117A LEU* 3.7 24.9 - - + +
118A ARG* 3.5 33.4 - - - +
121A ALA* 4.3 2.0 - - + +
140A TRP* 4.0 24.2 - - + -
142A ASN* 3.1 20.7 + - + +
143A HIS* 3.7 5.2 - - - +
145A ALA* 1.3 75.9 - - - +
147A PHE* 1.3 68.7 + - + +
149A SER* 2.6 22.9 + - - -
150A ALA* 3.6 4.5 + - - +
290B ARG 4.1 7.0 - - - +
291B ALA 3.5 25.4 - - - +
292B ASN 4.4 3.6 - - - +
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Residues in contact with PHE 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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117A LEU* 3.8 39.9 - - + -
120A ALA* 5.3 0.2 - - + -
121A ALA* 3.7 20.6 - - + -
124A LEU* 5.4 2.5 - - + -
133A VAL* 3.7 33.0 - - + -
135A VAL* 5.2 0.7 - - + -
143A HIS* 3.0 38.6 + + + -
146A ILE* 1.3 80.1 - - + +
148A ASN* 1.3 63.7 + - - +
150A ALA* 3.1 9.5 + - - +
151A GLY 3.5 0.2 + - - -
152A LEU* 3.0 34.7 + - + +
154A VAL* 3.6 19.7 - - + -
186A LEU* 3.7 26.0 - - + -
219A LEU* 4.1 16.2 - - + -
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Residues in contact with ASN 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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144A LYS* 2.9 54.4 + - - +
145A ALA* 3.9 4.9 - - - +
147A PHE* 1.3 75.6 - - - +
149A SER* 1.3 62.1 + - - +
151A GLY* 3.0 14.6 + - - -
152A LEU 2.9 19.8 - - - +
153A GLU* 4.1 1.6 - - - -
154A VAL* 3.7 15.1 + - - +
126B LYS* 4.7 3.9 + - - -
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Residues in contact with SER 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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118A ARG* 3.0 36.7 + - - -
145A ALA 2.9 18.5 + - - -
146A ILE 2.6 16.1 + - - -
148A ASN* 1.3 77.3 - - - +
150A ALA* 1.3 59.2 + - - +
151A GLY 3.2 1.3 + - - -
126B LYS* 3.9 23.5 + - - +
291B ALA* 3.6 18.1 + - - -
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Residues in contact with ALA 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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121A ALA* 3.6 36.6 - - + +
122A ASP* 3.5 24.5 - - - +
125A ALA* 3.2 23.1 - - + +
126A LYS* 4.9 5.1 + - - +
146A ILE 4.2 1.3 - - - +
147A PHE 3.1 7.1 + - - +
148A ASN 3.1 1.0 - - - -
149A SER* 1.3 78.9 + - - +
151A GLY* 1.3 59.4 + - - +
152A LEU* 3.4 2.5 - - + -
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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