Contacts of the helix formed by residues 150 - 155 (chain B) in PDB entry 4I6J
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 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A LEU* 5.5 13.0 - - + -
146B SER* 4.3 13.2 - - - +
148B ALA 3.5 3.5 - - - +
149B ARG* 1.3 83.7 - - + +
151B SER* 1.3 58.4 + - - +
152B PHE* 3.2 3.6 - - - -
153B MET* 3.1 40.8 + - + +
154B ASP* 3.9 6.4 + - - +
181B ASP* 4.1 22.7 - - + +
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Residues in contact with SER 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 3.3 17.5 + - - +
118B ASP 2.7 21.6 + - - -
119B SER 3.4 23.8 - - - -
120B SER 3.7 14.8 - - - -
121B LYS* 4.2 0.7 - - - -
124B ALA* 3.4 12.3 - - - +
146B SER* 4.9 2.3 + - - -
149B ARG 2.7 5.9 + - - -
150B PRO* 1.3 68.9 - - - +
152B PHE* 1.3 64.4 + - - +
153B MET 3.1 0.4 - - - -
154B ASP* 3.0 29.3 + - - +
155B LEU* 3.7 3.3 + - - +
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 5.1 0.9 - - + -
117B VAL* 4.1 32.8 - - + -
124B ALA* 3.9 17.3 - - + -
127B ALA* 4.1 19.3 - - + -
128B CYS* 5.0 2.2 - - - -
131B LEU* 5.8 1.3 - - + -
144B LEU* 4.2 37.5 - - + -
145B ILE 4.6 0.7 - - - -
146B SER* 3.7 22.9 - - - -
150B PRO 3.2 0.6 - - - -
151B SER* 1.3 79.5 + - - +
153B MET* 1.3 61.7 + - - +
155B LEU* 3.2 23.9 + - + +
160B PHE* 3.6 29.4 - + + -
180B ASP 5.3 0.7 - - - -
181B ASP 3.9 12.8 - - - +
182B THR* 4.4 7.9 - - - +
183B PRO* 3.7 24.3 - - + +
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Residues in contact with MET 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PRO* 3.1 26.8 + - + +
152B PHE* 1.3 77.1 - - - +
154B ASP* 1.3 62.9 + - - +
155B LEU 3.3 7.1 + - - +
181B ASP* 3.4 12.1 - - - +
182B THR 3.3 24.9 - - - +
183B PRO* 3.5 29.1 - - - +
207B SER* 3.6 5.6 - - - +
209B PRO* 3.1 41.7 - - + -
210B HIS* 5.4 3.4 - - - -
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B SER 4.3 6.8 - - - +
121B LYS* 3.4 42.0 + - + +
149B ARG* 5.8 2.3 - - - +
150B PRO 4.4 4.2 - - - +
151B SER* 3.0 30.0 + - - +
153B MET* 1.3 79.3 - - - +
155B LEU* 1.3 61.4 + - - +
156B PRO* 3.9 1.7 - - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LYS* 4.4 6.5 - - + +
124B ALA* 4.0 20.2 - - + +
125B GLU* 3.2 46.2 - - + +
128B CYS* 3.5 28.0 - - - -
152B PHE* 3.2 25.1 + - + +
153B MET 3.6 8.3 - - - +
154B ASP* 1.3 80.9 - - - +
156B PRO* 1.3 79.5 - - + +
157B LYS* 3.5 2.6 + - - -
159B HIS* 4.6 8.1 - - + +
160B PHE* 4.0 16.2 - - + +
183B PRO* 5.5 2.1 - - - +
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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