Contacts of the helix formed by residues 87 - 95 (chain C) in PDB entry 1P4D
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 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C SER 4.6 1.6 - - - +
86C ALA* 1.3 88.8 - - + +
88C LYS* 1.3 65.6 + - - +
90C VAL* 3.0 33.3 + - + +
91C SER* 3.0 18.9 + - - -
200C TYR* 5.0 4.9 - - + +
201C ARG* 5.4 7.6 - - + -
204C LEU* 4.9 5.2 - - + -
224C TRP* 3.2 39.3 - - + +
225C GLU* 2.9 20.6 - - - +
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA 3.4 3.0 + - - +
87C PRO* 1.3 72.2 - - - +
89C SER* 1.3 64.2 + - - +
91C SER* 3.3 3.7 + - - -
92C MET* 3.0 43.2 + - + +
149C SER* 6.0 0.2 - - - -
153C GLU* 3.4 16.9 - - - +
154C PRO* 2.9 46.0 - - - +
155C GLN* 4.9 9.6 - - + +
225C GLU* 3.2 15.4 + - - +
231C VAL* 3.7 13.0 - - + +
234C PHE* 2.8 45.8 + - + +
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Residues in contact with SER 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LYS* 1.3 77.1 - - - +
90C VAL* 1.3 62.9 + - - +
92C MET* 3.3 14.5 - - - +
93C MET* 3.0 22.0 + - - +
225C GLU* 3.0 21.3 + - - -
226C MET* 2.7 53.9 + - - +
229C VAL* 4.0 18.8 - - - +
231C VAL* 4.1 4.7 - - - +
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Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA* 4.3 14.1 - - + -
87C PRO* 3.0 33.2 + - + +
89C SER* 1.3 77.0 + - - +
91C SER* 1.3 60.1 + - - +
92C MET 2.9 1.3 - - - -
93C MET* 2.8 2.4 + - - +
94C ALA* 2.6 35.7 + - + +
102C LEU* 4.4 22.7 - - + +
106C HIS* 6.1 0.4 - - + -
156C LEU* 5.0 5.2 - - + -
204C LEU* 4.3 13.9 - - + -
208C VAL* 4.6 5.4 - - + -
224C TRP* 3.7 18.8 - - + -
226C MET* 3.3 18.6 - - + -
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 3.8 8.1 + - - +
87C PRO 3.0 12.9 + - - -
88C LYS* 3.7 4.4 - - - -
90C VAL* 1.3 74.9 - - - +
92C MET* 1.3 59.5 + - - +
94C ALA* 4.3 2.7 - - - -
95C MET* 2.9 35.9 + - - +
154C PRO* 3.0 29.5 + - - -
155C GLN* 3.5 1.7 - - - -
156C LEU* 2.7 41.5 + - - +
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Residues in contact with MET 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LYS* 3.0 41.0 + - + +
89C SER* 3.3 13.7 - - - +
90C VAL 2.9 0.4 - - - -
91C SER* 1.3 75.3 - - - +
93C MET* 1.3 61.5 + - - +
95C MET 2.2 24.8 - - - +
96C LEU* 3.0 25.7 - - + +
97C GLY* 3.2 1.9 + - - -
154C PRO* 4.5 11.4 - - + -
229C VAL* 3.6 20.9 - - + -
230C PRO* 3.7 5.6 - - - +
231C VAL* 3.4 30.5 - - + -
234C PHE* 3.3 37.2 - - + -
281C LEU* 6.1 1.8 - - + -
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Residues in contact with MET 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C SER 3.0 5.5 + - - +
90C VAL 2.8 4.6 + - - +
92C MET* 1.3 71.2 - - - +
94C ALA* 1.3 71.0 + - - +
96C LEU* 6.0 0.4 - - + -
97C GLY* 3.2 23.8 - - - +
98C GLY 3.6 0.2 + - - -
99C ASP* 3.6 8.4 + - + +
102C LEU* 3.5 6.1 - - + -
213C TYR* 3.6 34.8 - - + +
226C MET* 3.4 24.0 - - + -
229C VAL* 5.0 6.1 - - - -
286C PHE* 5.1 5.4 - - + -
288C ILE* 3.4 46.2 - - + +
291C TYR* 3.6 31.9 - - - -
292C ARG* 5.2 4.9 - - + -
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C VAL* 2.6 21.2 + - + +
91C SER* 3.8 7.2 - - - +
93C MET* 1.3 78.4 - - - +
95C MET* 1.3 61.5 + - + +
98C GLY 3.0 19.9 + - - +
99C ASP 3.1 21.2 - - - +
100C LYS* 4.6 1.7 - - - +
102C LEU* 3.2 18.3 - - + +
103C ILE* 4.2 19.5 - - + -
156C LEU* 4.4 10.5 - - + -
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Residues in contact with MET 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.4 28.7 - - + +
26C LEU* 4.1 19.5 - - + -
91C SER 2.9 22.1 + - - +
92C MET 2.2 33.1 - - - +
94C ALA* 1.3 75.3 - - - +
96C LEU* 1.3 62.8 + - + +
97C GLY 2.4 9.7 + - - -
100C LYS* 5.8 6.3 - - - +
103C ILE* 5.3 1.3 - - - +
147C ASP* 3.4 44.4 - - + +
154C PRO* 4.5 12.6 - - + -
156C LEU* 3.7 32.8 - - + +
277C TRP* 4.5 4.0 - - - -
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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