Contacts of the helix formed by residues 87 - 95 (chain S) in PDB entry 1M5N
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 ALA 87 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S PRO* 5.5 8.5 - - + -
35S THR 6.0 0.2 - - - +
38S VAL* 3.4 27.4 - - + -
80S TRP* 4.8 2.0 - - + -
83S ILE* 6.0 1.1 - - + -
84S ASP* 3.2 14.7 + - - +
86S ASN* 1.3 77.9 - - + +
88S ARG* 1.3 54.8 + - - +
90S GLU* 2.7 18.2 + - - +
91S VAL* 2.7 37.6 + - + +
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Residues in contact with ARG 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80S TRP* 3.3 50.8 + - + +
81S LEU* 4.0 17.2 + - - +
83S ILE* 4.1 17.5 + - + -
84S ASP 3.1 17.5 - - - +
85S ALA* 3.0 34.0 - - - +
86S ASN 3.4 0.4 - - - -
87S ALA* 1.3 75.5 - - - +
89S ARG* 1.3 57.1 + - - +
90S GLU 2.8 9.7 + - - -
91S VAL* 3.0 1.7 + - - +
92S LYS* 2.8 41.8 + - - +
120S GLU* 4.5 13.2 + - - -
125S GLN* 5.2 15.2 + - - +
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Residues in contact with ARG 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85S ALA* 4.3 20.9 + - - +
86S ASN 4.0 9.7 + - - +
87S ALA 3.3 0.2 - - - -
88S ARG* 1.3 81.4 - - - +
90S GLU* 1.3 59.0 + - - +
92S LYS* 4.3 12.0 - - - +
93S ASN* 3.7 24.7 + - - +
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Residues in contact with GLU 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S VAL* 3.3 30.8 - - + +
42S ARG* 4.0 6.2 + - - -
86S ASN 3.8 5.5 + - - +
87S ALA* 2.7 29.1 + - - +
89S ARG* 1.3 79.1 - - - +
91S VAL* 1.3 63.1 - - - +
92S LYS 3.3 0.2 - - - -
93S ASN* 3.1 14.6 + - - +
94S TYR* 3.2 38.3 + - + -
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Residues in contact with VAL 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S LEU* 4.6 2.0 - - + -
38S VAL* 4.0 22.9 - - + +
41S SER* 3.0 35.2 - - - +
61S ILE* 5.2 10.1 - - + -
80S TRP* 3.6 34.1 - - + -
87S ALA 2.7 19.0 + - - +
90S GLU* 1.3 65.3 - - - +
92S LYS* 1.3 55.7 + - - +
93S ASN 2.5 17.6 + - - -
94S TYR* 3.0 5.9 + - - -
95S VAL* 3.0 32.9 - - + +
116S ILE* 4.4 12.3 - - + -
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Residues in contact with LYS 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80S TRP* 3.8 26.0 - - + +
88S ARG* 2.8 38.6 + - - +
89S ARG* 4.3 10.8 - - - +
91S VAL* 1.3 75.3 - - - +
93S ASN* 1.3 60.6 + - - +
95S VAL* 4.9 1.8 - - - -
96S LEU* 3.0 35.3 - - - +
116S ILE* 4.4 4.7 - - + -
120S GLU* 2.7 41.9 + - - +
125S GLN 4.1 6.9 + - - -
126S TRP* 3.4 48.6 - - + +
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Residues in contact with ASN 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89S ARG* 3.7 19.8 + - - +
90S GLU* 3.1 9.6 + - - +
91S VAL 2.5 7.7 + - - -
92S LYS* 1.3 78.0 + - - +
94S TYR* 1.3 57.3 + - + +
95S VAL 2.9 9.7 + - - -
96S LEU* 3.5 13.3 + - - +
97S GLN* 3.5 43.7 + - - +
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Residues in contact with TYR 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S VAL* 5.0 1.8 - - + -
41S SER* 3.0 42.7 - - - +
42S ARG* 3.1 52.0 + - + -
45S ALA* 3.4 17.0 - - + +
90S GLU* 3.2 48.6 + - + -
91S VAL 3.0 2.7 + - - +
93S ASN* 1.3 78.8 - - + +
95S VAL* 1.3 51.9 + - - +
97S GLN* 4.4 4.9 - - - -
98S THR* 2.6 22.2 + - - -
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Residues in contact with VAL 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S SER* 4.7 7.6 - - - +
44S LEU* 4.9 7.2 - - + -
61S ILE* 5.9 2.0 - - + -
91S VAL* 3.0 36.1 - - + +
92S LYS* 4.8 0.9 - - - -
93S ASN 2.9 0.6 - - - -
94S TYR* 1.3 83.3 - - + +
96S LEU* 1.3 63.5 + - + +
97S GLN 2.8 8.0 + - - -
98S THR* 2.8 14.9 + - - +
99S LEU* 2.8 22.2 - - - +
109S ALA* 4.3 7.6 - - + +
112S CYS* 3.5 32.3 - - - -
113S VAL* 3.7 18.2 - - + -
116S ILE* 5.8 2.9 - - + -
126S TRP* 6.2 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
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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