Contacts of the helix formed by residues 98 - 116 (chain A) in PDB entry 4R4N
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 ASN 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASN 3.8 7.6 + - - +
95A MET* 3.8 17.3 + - - +
96A TRP 3.8 1.6 + - - -
97A LYS* 1.3 75.8 - - - +
99A ASN* 1.3 61.0 + - - +
100A MET* 3.2 30.6 + - - +
101A VAL* 2.8 35.3 + - + +
102A GLU* 3.9 1.4 + - - +
480A ARG* 5.3 1.2 - - - +
483A LEU* 3.4 22.8 + - - +
484A TYR* 4.9 2.6 + - - +
486A TYR 3.0 25.3 + - - +
487A LYS* 4.5 5.2 - - - +
488A VAL* 5.0 1.7 + - - +
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 3.3 44.2 + - - +
50A THR 4.1 0.5 - - - +
52A LEU* 5.2 0.3 - - - +
97A LYS 4.2 1.2 + - - -
98A ASN* 1.3 74.2 + - - +
100A MET* 1.3 63.1 + - + +
102A GLU* 3.2 16.3 + - - +
103A GLN* 2.4 53.6 + - - +
488A VAL* 6.3 1.1 - - + -
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Residues in contact with MET 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.1 24.5 - - + -
98A ASN* 2.9 33.5 + - - +
99A ASN* 1.3 78.8 - - + +
101A VAL* 1.3 61.5 + - - +
103A GLN* 3.4 8.6 + - - +
104A MET* 3.0 24.4 + - - +
217A TYR* 5.7 7.3 - - + -
225A ILE* 4.7 8.7 - - - -
248A THR* 5.1 4.3 - - - -
483A LEU* 3.4 22.6 - - + +
486A TYR* 3.4 34.1 - - + -
487A LYS* 3.5 9.0 - - - +
488A VAL* 3.5 28.9 - - + -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET 4.5 0.4 - - - +
98A ASN* 2.8 24.8 + - + +
100A MET* 1.3 78.4 - - - +
102A GLU* 1.3 58.5 + - - +
104A MET* 3.2 5.4 + - - +
105A HIS* 3.0 27.2 + - - +
476A ARG* 4.2 30.5 - - + +
479A TRP* 4.6 7.4 - - + -
480A ARG* 3.9 44.0 - - + +
483A LEU* 3.7 24.2 - - + -
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN 3.9 0.8 + - - +
99A ASN* 3.2 21.5 + - - +
101A VAL* 1.3 79.9 - - - +
103A GLN* 1.3 63.1 + - + +
105A HIS* 3.5 10.5 + - - +
106A THR* 3.3 35.3 + - + +
476A ARG* 3.8 25.1 + - - +
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Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR 3.0 24.4 + - - -
51A THR* 3.9 9.5 - - - +
52A LEU* 3.4 35.0 + - - +
99A ASN* 2.4 43.7 + - - +
100A MET* 3.8 9.6 - - - +
101A VAL 3.2 0.2 - - - -
102A GLU* 1.3 76.3 - - + +
104A MET* 1.3 62.4 + - - +
106A THR* 2.6 23.1 + - - -
107A ASP* 3.3 16.9 + - - +
217A TYR* 4.7 9.3 - - + -
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Residues in contact with MET 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A MET 3.0 17.6 + - - +
101A VAL* 3.6 6.3 - - - +
103A GLN* 1.3 75.5 - - - +
105A HIS* 1.3 65.9 - - - +
107A ASP* 3.0 11.6 + - - +
108A ILE* 3.1 29.1 + - + +
215A ILE* 5.0 2.9 - - + -
217A TYR* 3.4 44.8 + - + +
251A ILE* 3.6 47.1 - - + -
253A PRO* 6.2 2.7 - - + -
479A TRP* 3.9 36.1 - - + +
483A LEU* 4.9 9.9 - - + -
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Residues in contact with HIS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL 3.0 13.6 + - - +
102A GLU* 3.6 18.4 - - - +
104A MET* 1.3 78.6 - - - +
106A THR* 1.3 63.1 + - + +
108A ILE* 3.6 2.6 + - - +
109A ILE* 3.2 49.5 + - + +
427A TRP* 4.3 19.9 + + - -
474A ASP* 4.6 0.7 - - - -
475A MET* 4.2 19.7 - - + -
476A ARG* 3.4 58.5 + - + +
479A TRP* 3.3 25.6 + - + +
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Residues in contact with THR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.3 28.2 + - + +
103A GLN* 2.6 25.7 + - - -
105A HIS* 1.3 78.3 - - + +
107A ASP* 1.3 65.5 + - - +
109A ILE* 3.5 12.7 + - + +
110A SER* 3.2 24.7 + - - -
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Residues in contact with ASP 107 (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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54A CYS* 5.9 0.3 - - - +
69A TRP* 4.5 20.1 - - + -
103A GLN* 3.5 11.3 - - - +
104A MET 3.0 6.1 + - - +
106A THR* 1.3 84.2 + - - +
108A ILE* 1.3 65.8 + - + +
110A SER* 3.1 10.9 + - - -
111A LEU* 3.0 24.9 + - - +
217A TYR* 2.5 36.6 + - - +
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Residues in contact with ILE 108 (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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69A TRP* 5.7 4.5 - - + -
104A MET* 3.1 31.0 + - + +
105A HIS 4.1 3.1 - - - +
107A ASP* 1.3 78.8 - - + +
109A ILE* 1.3 65.7 + - - +
111A LEU* 3.3 13.9 + - + +
112A TRP* 3.1 39.7 + - + +
215A ILE* 6.2 0.7 - - + -
217A TYR* 5.4 2.2 - - + +
253A PRO* 3.6 33.9 - - + -
255A VAL* 4.5 1.6 - - + -
427A TRP* 3.8 17.7 - - + -
479A TRP* 4.0 30.1 - - + -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS* 3.2 42.5 + - + +
106A THR* 3.6 13.0 - - + +
108A ILE* 1.3 79.2 - - - +
110A SER* 1.3 63.5 + - - +
112A TRP* 3.4 1.7 + - - +
113A ASP* 2.9 47.6 + - - +
427A TRP* 3.7 24.5 - - + -
428A GLN* 4.2 22.4 - - + +
429A ARG* 4.0 13.5 - - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 5.1 9.1 - - - -
106A THR 3.2 12.1 + - - -
107A ASP* 3.1 13.4 + - - -
109A ILE* 1.3 76.9 - - - +
111A LEU* 1.3 65.4 + - - +
113A ASP* 4.0 6.2 - - - +
114A GLN* 3.1 26.2 + - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL 4.6 0.7 - - - +
66A HIS* 3.6 38.1 - - + +
69A TRP* 3.5 56.0 - - + +
107A ASP 3.0 13.0 + - - +
108A ILE* 3.5 20.6 - - + +
109A ILE 3.2 0.2 - - - -
110A SER* 1.3 76.4 - - - +
112A TRP* 1.3 69.8 + - + +
114A GLN* 3.2 3.1 + - - +
115A SER* 2.8 46.9 + - - +
210A PHE* 5.1 1.8 - - + -
253A PRO* 5.6 8.1 - - + -
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Residues in contact with TRP 112 (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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66A HIS* 5.2 0.6 + - - -
108A ILE* 3.1 25.8 + - + +
109A ILE 3.9 3.4 - - - +
111A LEU* 1.3 93.1 - - + +
113A ASP* 1.3 60.1 + - - +
115A SER* 4.4 0.7 - - - -
116A LEU* 2.7 60.3 + - + +
210A PHE* 3.7 27.9 - + - -
253A PRO 4.9 3.6 + - - -
255A VAL* 3.6 38.9 - - + +
377A ASN* 3.8 27.8 - - + -
382A PHE* 4.2 15.3 - + - -
427A TRP* 3.4 36.1 - + + -
428A GLN* 4.0 16.6 - - - +
435A TYR* 4.6 5.4 - - - -
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Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 2.9 40.4 + - - +
110A SER* 4.0 5.8 - - - +
111A LEU 3.3 0.2 - - - -
112A TRP* 1.3 76.8 - - - +
114A GLN* 1.3 59.8 + - - +
116A LEU 4.7 3.4 - - - +
117A LYS* 3.2 26.1 + - - +
118A PRO* 5.6 1.9 - - - +
121A GLN* 5.0 6.4 + - - -
203A GLN* 4.8 2.1 + - - -
428A GLN* 3.9 18.1 + - - +
429A ARG* 3.3 21.4 + - - -
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 5.5 8.7 - - + -
110A SER 3.1 18.2 + - - +
111A LEU* 3.9 3.6 - - - +
113A ASP* 1.3 77.3 - - - +
115A SER* 1.3 61.7 + - - +
117A LYS* 3.5 32.3 + - - +
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Residues in contact with SER 115 (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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65A VAL* 3.5 50.9 + - - +
69A TRP* 4.9 3.5 - - - +
111A LEU* 2.8 32.1 + - - +
112A TRP* 4.0 1.8 - - - -
114A GLN* 1.3 82.5 - - - +
116A LEU* 1.3 64.5 + - - +
117A LYS* 3.5 7.8 + - - +
206A PRO 5.6 0.3 - - - +
208A VAL* 4.2 12.6 - - - +
210A PHE* 5.7 0.9 - - - -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TRP* 2.7 41.1 + - + +
113A ASP* 4.7 1.4 - - - +
115A SER* 1.3 72.3 - - - +
117A LYS* 1.3 61.6 + - - +
118A PRO* 3.2 13.9 - - - +
207A LYS* 6.1 1.1 - - - +
208A VAL* 3.5 28.3 - - + -
210A PHE* 3.7 30.1 - - + -
377A ASN* 3.6 26.9 - - - +
380A GLY* 4.5 15.9 - - - +
382A PHE* 4.5 4.9 - - + -
428A GLN* 5.6 1.0 + - - -
435A TYR* 3.6 25.4 + - + +
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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
------------------------------------------------------------
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