Contacts of the helix formed by residues 93 - 100 (chain B) in PDB entry 4PEI
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 SER 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B THR* 3.5 40.2 + - - +
49B LEU* 3.9 12.0 - - - +
54B ASP* 3.4 24.9 + - - +
57B TYR* 4.5 4.3 - - - -
92B GLU* 1.3 73.0 + - - +
94B SER* 1.3 63.1 + - - +
95B ASN* 2.6 22.4 + - - -
96B VAL* 3.0 17.6 + - - +
97B LEU* 3.2 11.6 + - - +
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Residues in contact with SER 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 3.7 14.7 + - - -
92B GLU* 3.0 23.2 + - - +
93B SER* 1.3 73.8 - - - +
95B ASN* 1.3 58.2 + - - +
97B LEU* 3.4 6.4 + - - +
98B LEU* 3.0 28.9 + - - +
151B VAL* 5.3 2.5 - - - -
154B LEU* 3.6 36.7 - - - +
155B PHE* 4.1 20.7 - - - +
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Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 3.3 6.1 - - - +
54B ASP* 2.9 24.4 + - - -
57B TYR* 3.4 41.3 - - + +
93B SER* 2.6 27.9 + - - -
94B SER* 1.3 69.4 - - - +
96B VAL* 1.3 70.0 + - - -
98B LEU* 3.1 4.6 + - - +
99B HIS* 3.1 28.3 + - - -
146B PRO* 3.8 15.1 - - + +
154B LEU* 4.7 0.4 - - - -
402B SO4 3.2 30.4 + - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 3.6 27.1 - - - +
50B ARG* 3.6 36.8 - - - +
54B ASP* 4.2 0.2 - - - +
70B PHE* 6.4 0.2 - - + -
93B SER* 3.3 25.8 - - - +
95B ASN* 1.3 83.7 + - - +
97B LEU* 1.3 69.8 + - + +
99B HIS* 3.2 20.2 + - - +
100B LEU* 3.2 14.1 + - + +
106B VAL* 4.2 10.3 - - + -
333B PHE* 3.8 21.7 - - + -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 4.0 18.8 - - - +
86B PHE* 4.4 8.7 - - + -
88B GLY* 3.8 17.7 - - - -
92B GLU* 3.6 40.8 - - + +
93B SER 3.2 10.9 + - - +
94B SER* 4.0 7.4 - - - +
95B ASN 3.3 0.2 - - - -
96B VAL* 1.3 81.3 - - + +
98B LEU* 1.3 60.6 + - - +
100B LEU 3.2 4.6 - - - +
101B TYR* 3.1 21.1 + - - +
106B VAL* 4.9 1.8 - - + -
112B TYR* 3.6 45.2 + - + +
115B VAL* 5.7 0.5 - - - +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER 3.0 17.7 + - - +
95B ASN* 3.1 6.7 + - - +
97B LEU* 1.3 76.1 - - - +
99B HIS* 1.3 66.4 + - - +
101B TYR* 3.1 25.3 + - + +
115B VAL* 5.9 0.4 - - + -
142B TYR* 4.1 33.9 - - + -
143B THR 3.6 24.5 - - - +
144B TYR* 3.9 18.4 - - + -
146B PRO* 4.2 12.3 - - + -
154B LEU* 3.7 8.5 - - + -
292B PHE* 4.1 13.9 - - + -
337B PHE* 4.2 2.4 - - - -
403B PG4 3.6 17.3 - - - +
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Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 4.8 5.4 - - - -
95B ASN 3.1 24.0 + - - -
96B VAL* 3.6 7.0 - - - +
98B LEU* 1.3 76.7 - - - +
100B LEU* 1.3 61.4 + - - +
101B TYR* 3.4 2.9 + - - -
102B ASN 5.0 0.3 + - - -
144B TYR* 2.6 39.7 + + - -
145B PRO* 5.1 2.5 - - + -
146B PRO* 3.8 15.2 - - + +
333B PHE* 3.6 31.0 - - + +
334B ASP* 3.7 22.4 + - + +
337B PHE* 3.4 28.6 - - - +
402B SO4 2.7 35.4 + - - -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.2 17.5 + - + +
97B LEU 3.2 3.4 - - - -
98B LEU 3.1 0.6 - - - -
99B HIS* 1.3 82.1 - - - +
101B TYR* 1.3 54.7 + - - -
102B ASN* 3.0 3.8 - - - +
103B GLY* 2.6 41.8 + - - +
104B GLY* 3.9 17.9 - - - +
105B PHE 4.2 0.2 - - - +
106B VAL* 3.7 29.6 - - + -
112B TYR* 3.3 20.7 - - + -
333B PHE* 3.9 38.4 - - + -
336B GLN* 4.0 23.6 - - + +
337B PHE 5.4 0.2 - - - +
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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
------------------------------------------------------------
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