Contacts of the helix formed by residues 93 - 100 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A THR* 3.4 33.2 + - - +
49A LEU* 3.8 18.3 - - - +
54A ASP* 3.4 20.5 - - - +
57A TYR* 4.4 6.3 - - - -
92A GLU* 1.3 72.0 + - - +
94A SER* 1.3 63.7 + - - +
95A ASN* 2.7 22.0 + - - -
96A VAL* 3.0 20.8 + - - +
97A LEU* 3.4 11.8 + - - +
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Residues in contact with SER 94 (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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57A TYR* 3.6 16.4 + - - -
92A GLU* 3.0 25.2 + - - +
93A SER* 1.3 71.2 - - - +
95A ASN* 1.3 63.0 + - - +
97A LEU* 3.3 7.5 + - - +
98A LEU* 3.1 23.9 + - - +
151A VAL* 5.3 2.7 - - - -
154A LEU* 3.6 35.8 - - - +
155A PHE* 4.0 21.1 - - - +
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Residues in contact with ASN 95 (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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50A ARG* 3.3 2.8 - - - +
54A ASP* 2.9 25.1 + - - -
57A TYR* 3.4 43.8 - - + +
93A SER* 2.7 26.9 + - - -
94A SER* 1.3 73.5 - - - +
96A VAL* 1.3 67.5 + - - -
98A LEU* 3.3 5.1 + - - +
99A HIS* 3.1 28.6 + - - -
146A PRO* 3.8 18.2 - - + +
154A LEU* 4.8 0.2 - - - -
402A SO4 3.0 30.0 + - - +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 3.9 26.9 - - - +
50A ARG* 3.7 35.4 - - - +
93A SER* 3.0 25.7 + - - +
95A ASN* 1.3 84.8 + - - +
97A LEU* 1.3 66.0 + - + +
99A HIS* 3.4 11.6 + - - +
100A LEU* 3.1 23.7 + - + +
106A VAL* 4.2 11.7 - - + -
333A PHE* 3.4 27.3 - - + -
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Residues in contact with LEU 97 (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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48A THR* 4.3 14.4 - - + +
86A PHE* 4.3 11.2 - - + -
88A GLY* 4.0 15.7 - - - -
92A GLU* 3.6 42.8 - - + +
93A SER 3.4 9.6 + - - +
94A SER* 3.3 8.8 + - - +
96A VAL* 1.3 82.0 - - + +
98A LEU* 1.3 57.9 + - - +
100A LEU* 3.0 25.5 - - + -
101A TYR* 3.0 3.5 + - - +
106A VAL* 4.9 2.0 - - + -
112A TYR* 3.4 48.6 + - + +
115A VAL* 5.8 0.3 - - - +
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Residues in contact with LEU 98 (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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94A SER 3.1 13.2 + - - +
95A ASN* 3.6 8.3 - - - +
97A LEU* 1.3 72.5 - - - +
99A HIS* 1.3 67.1 + - - +
100A LEU 3.0 1.3 - - - -
101A TYR* 3.0 28.5 + - + +
142A TYR* 3.8 42.0 - - + -
143A THR 3.5 23.1 - - - +
144A TYR* 3.6 20.6 - - + -
146A PRO* 3.9 21.8 - - + -
154A LEU* 4.1 15.0 - - + -
292A PHE* 4.4 10.8 - - + -
337A PHE* 4.0 2.9 - - - -
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Residues in contact with HIS 99 (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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50A ARG* 4.8 2.2 - - - -
95A ASN 3.1 22.7 + - - -
96A VAL* 3.6 10.3 - - - +
98A LEU* 1.3 78.3 - - - +
100A LEU* 1.3 60.9 + - - +
101A TYR* 3.5 2.9 + - - -
102A ASN 5.1 0.2 + - - -
144A TYR* 2.5 40.4 + + - -
145A PRO* 5.1 2.2 - - + -
146A PRO* 3.6 11.2 - - + +
333A PHE* 3.5 30.1 - - + +
334A ASP* 3.6 20.2 + - + +
336A GLN 4.9 0.2 - - - -
337A PHE* 3.1 29.5 - - - +
402A SO4 2.8 41.6 + - - -
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Residues in contact with LEU 100 (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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96A VAL* 3.1 15.6 + - + +
97A LEU* 3.0 6.1 + - - -
98A LEU 3.0 1.0 - - - -
99A HIS* 1.3 81.2 - - - +
101A TYR* 1.3 55.3 + - - +
102A ASN 3.0 4.0 - - - +
103A GLY 2.6 39.0 + - - +
104A GLY* 4.1 13.5 - - - +
105A PHE 4.2 4.9 - - - +
106A VAL* 3.7 29.2 - - + -
112A TYR* 3.2 24.2 - - + -
333A PHE* 4.1 29.8 - - + -
336A GLN* 4.1 31.4 - - + +
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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