Contacts of the helix formed by residues 94 - 104 (chain N) in PDB entry 2DYS
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 PHE 94 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92N MET 4.3 0.4 - - - -
93N ALA* 1.3 88.5 - - + +
95N PRO* 1.3 58.7 - - - +
96N ARG 3.1 0.5 + - - -
97N MET* 3.2 29.5 + - + -
98N ASN 3.0 22.9 + - - -
162N ILE* 4.2 5.2 - - + -
163N ASN* 3.1 23.3 + - - +
166N THR* 3.7 25.8 - - + -
609N PGV 3.1 46.2 - - - +
75P VAL 5.6 0.4 - - - -
78P GLY* 3.4 25.6 - - - -
79P LEU* 3.5 30.3 - - + -
82P GLY* 4.0 13.2 - - - -
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Residues in contact with PRO 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N THR* 3.3 41.1 - - - +
15N ILE* 3.9 3.1 - - - +
91N ASP* 3.8 17.0 - - + +
92N MET* 3.2 13.2 - - + +
93N ALA 3.2 11.9 - - - +
94N PHE* 1.3 83.4 - - - +
96N ARG* 1.3 57.7 + - - +
98N ASN* 3.6 10.2 - - + +
99N ASN* 3.4 14.2 + - - +
609N PGV 4.0 3.8 - - - +
9P HIS 4.4 10.5 - - - +
10P MET* 5.6 0.4 - - - -
11P VAL* 3.5 34.1 - - + +
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Residues in contact with ARG 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N THR* 4.7 6.9 - - + +
95N PRO* 1.3 75.6 - - - +
97N MET* 1.3 66.9 + - - +
98N ASN 3.1 1.3 - - - -
99N ASN* 3.0 12.3 + - - +
100N MET 3.2 2.3 + - - -
609N PGV 3.0 39.5 + - - +
11P VAL* 3.5 20.5 - - + +
12P ASN 4.9 0.4 + - - -
14P SER* 3.5 27.9 - - - -
16P TRP* 5.0 0.6 - - - -
17P PRO* 3.2 41.1 - - + +
57P TRP* 3.5 24.0 + - + +
60P ASP* 3.9 20.6 + - - +
61P VAL* 3.8 7.6 - - - +
64P GLU* 2.7 44.5 + - - -
20W VAL* 4.5 3.2 - - - +
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Residues in contact with MET 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N PHE* 3.6 26.5 - - + +
96N ARG* 1.3 75.9 - - - +
98N ASN* 1.3 62.9 + - - +
100N MET* 3.1 4.7 + - - +
101N SER* 3.1 21.6 + - - -
159N LEU* 3.2 57.3 - - + +
162N ILE* 3.7 27.8 - - + -
163N ASN* 4.0 5.4 - - + +
609N PGV 3.1 51.4 + - + +
57P TRP* 3.8 12.2 - - + -
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Residues in contact with ASN 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N HIS* 4.5 4.9 - - - +
15N ILE* 3.7 24.6 - - - +
19N TYR* 4.6 0.7 - - - -
80N ASN* 3.1 40.4 + - - +
91N ASP* 5.3 0.4 + - - -
92N MET* 3.9 14.6 - - + +
94N PHE 3.0 9.9 + - - +
95N PRO* 3.6 11.3 + - + +
96N ARG 3.1 0.2 - - - -
97N MET* 1.3 78.2 - - - +
99N ASN* 1.3 61.2 + - - +
101N SER* 3.2 24.3 + - - -
102N PHE 3.4 4.3 + - - -
159N LEU 6.1 0.2 - - - -
160N GLY* 5.4 3.1 - - - -
163N ASN* 3.0 24.7 + - - +
164N PHE* 5.8 0.9 - - - -
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Residues in contact with ASN 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N LEU 3.4 22.0 + - - -
8N PHE* 3.7 3.8 - - - +
9N SER* 3.1 37.8 + - - +
15N ILE* 3.6 20.8 - - + +
18N LEU* 4.8 3.8 - - - +
95N PRO 3.4 3.8 + - - +
96N ARG 3.0 11.9 + - - +
98N ASN* 1.3 78.2 - - - +
100N MET* 1.3 61.9 + - - +
102N PHE* 3.2 5.2 + - - +
103N TRP* 3.1 36.8 + - - -
14P SER 4.1 0.4 + - - -
17P PRO* 3.6 22.0 - - + +
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Residues in contact with MET 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N ARG 3.2 6.6 + - - +
97N MET* 3.1 10.5 + - + +
99N ASN* 1.3 73.0 - - - +
101N SER* 1.3 64.8 + - - +
102N PHE 3.0 2.0 - - - -
103N TRP 3.8 0.8 - - - +
104N LEU* 3.0 36.7 + - + +
159N LEU* 3.3 29.4 - - + -
609N PGV 3.8 47.3 - - + -
17P PRO* 3.6 31.4 - - + +
20P GLY* 4.5 2.7 - - - -
21P ALA* 4.4 10.1 - - + +
57P TRP* 3.8 29.4 - - + -
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Residues in contact with SER 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N TYR* 3.0 18.9 + - - -
97N MET 3.1 10.3 + - - -
98N ASN* 3.2 14.7 + - - -
100N MET* 1.3 75.8 - - - +
102N PHE* 1.3 62.0 + - - +
104N LEU* 3.8 2.4 + - - -
105N LEU* 3.8 3.1 - - - +
156N SER* 2.4 54.6 + - - +
159N LEU* 3.4 10.7 - - - +
160N GLY* 3.2 20.4 + - - -
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Residues in contact with PHE 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N ILE* 4.5 5.8 - - + -
18N LEU* 3.6 45.8 - - + -
19N TYR* 3.2 41.7 + + + -
22N PHE* 3.8 18.6 - + + -
98N ASN 3.4 4.1 + - - +
99N ASN* 3.2 9.9 + - - +
100N MET 3.0 0.2 - - - -
101N SER* 1.3 82.7 - - - +
103N TRP* 1.3 104.5 + + - +
104N LEU 3.1 0.4 - - - -
105N LEU* 3.0 21.1 + - + +
106N PRO* 3.3 15.6 - - + +
606N TGL 3.9 20.9 - - + -
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Residues in contact with TRP 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N TRP 3.1 25.4 + - - -
7N LEU* 3.6 36.1 + - + -
18N LEU* 4.3 2.0 - - + +
99N ASN* 3.1 47.8 + - - +
100N MET 3.2 1.7 + - - +
102N PHE* 1.3 107.4 - + - +
104N LEU* 1.3 57.4 + - - +
105N LEU 3.2 0.4 - - - -
106N PRO* 3.5 19.7 - - + +
107N PRO* 2.8 27.6 - - + +
606N TGL 4.4 18.6 - - + -
17P PRO 4.5 3.6 - - - +
18P LEU* 4.0 30.1 - - + -
21P ALA* 3.4 22.1 - - + +
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Residues in contact with LEU 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100N MET* 3.0 26.3 + - + +
102N PHE 3.1 0.6 - - - -
103N TRP* 1.3 78.6 - - - +
105N LEU* 1.3 59.6 + - - +
107N PRO* 3.3 5.4 - - + +
108N SER* 3.0 28.6 + - - -
152N LEU* 4.0 21.3 - - + +
155N VAL* 3.9 18.2 - - + -
156N SER* 3.7 39.0 - - - +
159N LEU* 4.2 10.1 - - + -
609N PGV 4.5 7.9 - - + -
21P ALA* 3.9 13.2 - - - +
24P ALA* 3.7 30.1 - - + -
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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