Contacts of the strand formed by residues 116 - 121 (chain D) 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 CYS 116 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR 4.8 3.6 - - - +
102D ASN* 6.0 0.9 - - - -
113D LEU 3.7 5.6 - - - +
114D GLY 4.0 2.5 - - - -
115D VAL* 1.3 85.3 + - - +
117D SER* 1.3 68.8 + - - +
128D GLY 3.2 16.6 - - - +
129D VAL* 4.5 2.0 - - - -
160D TYR* 5.4 1.3 - - - -
161D VAL* 3.8 29.2 - - + -
164D MET* 4.1 14.8 - - - -
165D LEU* 3.9 18.8 - - + -
275D TRP* 3.1 32.0 - - - -
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASN 6.3 1.3 - - - -
111D TYR* 5.1 2.4 + - - -
113D LEU* 2.8 34.9 + - - +
116D CYS* 1.3 80.9 - - - +
118D CYS* 1.3 64.6 + - - +
119D ILE* 4.4 4.2 - - - +
126D ILE 4.0 0.2 - - - +
127D VAL* 3.2 6.4 - - - +
128D GLY* 2.9 27.6 + - - +
165D LEU* 4.3 6.3 - - - -
275D TRP* 3.3 34.8 - - - -
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Residues in contact with CYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D SER* 1.3 78.1 + - - +
119D ILE* 1.3 73.5 + - - +
125D ARG* 4.1 11.0 - - - -
126D ILE 3.1 17.3 - - - -
127D VAL* 3.9 18.6 - - + -
168D LEU* 4.1 8.7 - - + -
174D ILE* 4.2 7.9 - - - -
271D TYR* 4.7 0.9 - - - -
272D ASP* 3.3 44.7 + - + +
275D TRP* 3.7 23.0 - - + +
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Residues in contact with ILE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU* 4.0 14.1 - - + -
111D TYR* 4.0 18.4 - - + +
113D LEU* 4.1 17.5 - - + -
117D SER* 4.4 4.0 - - - +
118D CYS* 1.3 77.9 - - - +
120D ASN* 1.3 85.9 + - - +
121D ILE* 3.8 16.8 - - + +
125D ARG* 3.6 1.0 - - - -
126D ILE* 2.7 59.3 + - + +
269D LEU* 3.9 13.7 - - + -
270D GLU 3.6 7.6 - - - +
271D TYR* 5.3 1.1 - - + -
272D ASP* 4.1 0.7 - - - +
326D ILE* 3.8 23.6 - - + -
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Residues in contact with ASN 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 1.3 83.2 - - - +
121D ILE* 1.3 63.0 + - - +
123D GLY* 6.1 1.6 - - - +
124D LEU 3.4 6.7 - - - +
125D ARG* 3.8 11.9 - - - +
267D THR* 5.9 2.2 - - + -
268D ASP 3.7 2.4 - - - +
269D LEU* 3.4 2.6 - - - +
270D GLU* 2.7 56.0 + - + +
271D TYR 3.9 4.8 + - - -
272D ASP* 2.9 40.1 + - - +
273D LYS* 4.3 16.4 - - - +
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D SER 5.6 0.7 - - - +
39D PHE* 3.5 48.2 - - + -
83D LEU* 3.8 29.2 - - + -
85D LEU* 4.5 2.9 - - + -
119D ILE* 3.8 18.4 - - + +
120D ASN* 1.3 75.8 - - - +
122D ASN* 1.3 71.4 + - - +
123D GLY 3.1 2.5 - - - -
124D LEU* 2.8 34.2 + - + +
126D ILE* 4.0 7.2 - - + -
267D THR* 3.6 16.4 - - - +
268D ASP* 4.4 1.3 - - - -
269D LEU* 4.4 11.9 - - + +
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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