Contacts of the helix formed by residues 94 - 104 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A MET 4.4 0.2 - - - -
93A ALA* 1.3 88.2 - - + +
95A PRO* 1.3 57.8 - - - +
96A ARG 3.1 0.3 + - - -
97A MET* 3.2 30.4 + - + -
98A ASN 2.9 14.4 + - - -
162A ILE* 4.2 6.3 - - + -
163A ASN* 2.9 31.9 + - - +
166A THR* 3.6 27.4 - - + -
607A PGV 3.1 45.3 - - - +
75C VAL 5.5 0.7 - - - -
78C GLY* 3.4 28.0 - - - -
79C LEU* 3.9 25.1 - - + -
82C GLY* 4.0 15.9 - - - -
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Residues in contact with PRO 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.2 41.8 - - - +
15A ILE* 3.8 2.8 - - - +
91A ASP* 3.5 17.3 - - + +
92A MET* 3.3 11.2 - - + +
93A ALA 3.2 12.1 - - - +
94A PHE* 1.3 85.3 - - - +
96A ARG* 1.3 59.0 + - - +
98A ASN* 3.5 10.7 - - + +
99A ASN* 3.4 13.5 + - - +
163A ASN* 4.8 0.4 - - - +
607A PGV 3.9 2.9 - - - +
9C HIS 4.4 8.3 - - - +
10C MET* 5.5 0.4 - - - -
11C VAL* 3.6 34.8 - - + +
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Residues in contact with ARG 96 (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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10A THR* 4.4 11.4 - - + +
95A PRO* 1.3 76.0 - - - +
97A MET* 1.3 66.7 + - - +
98A ASN 3.1 1.3 - - - -
99A ASN* 3.0 11.2 + - - +
100A MET 3.2 1.9 + - - -
607A PGV 3.0 38.0 + - - +
11C VAL* 3.4 15.5 - - + +
12C ASN 5.0 0.2 + - - -
14C SER* 3.4 31.7 + - - -
16C TRP* 5.1 1.0 - - - -
17C PRO* 3.2 43.4 - - + +
57C TRP* 3.6 20.8 - - + +
60C ASP* 4.1 16.2 + - - +
61C VAL* 3.6 13.5 - - - +
64C GLU* 2.8 42.7 + - - -
20J VAL* 4.6 3.2 - - - +
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 3.6 35.2 - - + +
96A ARG* 1.3 75.7 - - - +
98A ASN* 1.3 61.4 + - - +
100A MET* 3.1 4.5 + - - +
101A SER* 3.1 22.3 + - - -
159A LEU* 3.2 57.6 - - + +
162A ILE* 4.0 16.8 - - + -
163A ASN* 4.1 5.8 - - + +
607A PGV 3.1 54.7 + - + +
57C TRP* 3.9 13.4 - - + -
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Residues in contact with ASN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A HIS* 4.4 5.3 - - - +
15A ILE* 3.8 24.9 - - - +
19A TYR* 4.8 0.5 + - - -
80A ASN* 3.0 40.7 + - - +
91A ASP* 5.1 0.2 + - - -
92A MET* 3.7 15.7 - - - +
94A PHE 2.9 9.5 + - - +
95A PRO* 3.5 11.2 + - + +
97A MET* 1.3 77.1 - - - +
99A ASN* 1.3 60.2 + - - +
101A SER* 3.2 23.7 + - - -
102A PHE 3.4 4.0 + - - -
160A GLY* 5.5 2.9 - - - -
163A ASN* 3.1 25.4 + - - +
164A PHE* 5.6 1.6 - - - -
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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
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7A LEU 3.3 24.9 + - - -
8A PHE* 4.0 2.4 - - - +
9A SER* 3.2 35.9 + - - +
15A ILE* 3.6 23.7 - - + +
18A LEU* 4.4 4.9 - - - +
95A PRO 3.4 3.6 + - - +
96A ARG 3.0 10.6 + - - +
98A ASN* 1.3 81.3 - - - +
100A MET* 1.3 60.8 + - - +
102A PHE* 3.2 4.0 + - - +
103A TRP* 3.1 40.1 + - - -
17C PRO* 3.8 16.5 - - + +
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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
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96A ARG 3.2 4.8 + - - -
97A MET* 3.1 10.3 + - + +
99A ASN* 1.3 73.2 - - - +
101A SER* 1.3 64.8 + - - +
102A PHE 3.0 1.6 - - - -
103A TRP 3.2 1.1 + - - +
104A LEU* 3.1 37.4 + - + +
159A LEU* 3.4 27.8 - - + -
607A PGV 3.8 43.5 - - + -
17C PRO* 3.6 31.8 - - + +
20C GLY* 4.4 11.4 - - - -
21C ALA* 4.4 2.0 - - + +
57C TRP* 3.7 32.1 - - + -
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Residues in contact with SER 101 (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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19A TYR* 3.0 18.6 + - - -
97A MET 3.1 12.6 + - - -
98A ASN* 3.3 15.0 + - - -
100A MET* 1.3 76.0 - - - +
102A PHE* 1.3 60.4 + - - +
104A LEU* 3.8 3.2 + - - +
105A LEU* 4.0 3.3 - - - +
156A SER* 2.4 54.0 + - - +
159A LEU* 3.6 6.9 - - - +
160A GLY* 3.3 19.8 + - - -
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.3 7.4 - - + -
18A LEU* 3.6 41.1 - - + -
19A TYR* 3.3 43.7 + + + -
22A PHE* 3.9 17.9 - + + -
98A ASN 3.4 4.1 + - - +
99A ASN* 3.2 9.3 + - - +
100A MET 3.0 0.4 - - - -
101A SER* 1.3 83.1 - - - +
103A TRP* 1.3 110.1 + + - +
104A LEU 3.1 0.4 - - - -
105A LEU* 3.1 16.0 + - + +
106A PRO* 3.3 16.3 - - + +
101L TGL 3.9 21.5 - - + -
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Residues in contact with TRP 103 (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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6A TRP 3.4 22.6 + - - -
7A LEU* 3.7 38.4 + - + -
18A LEU* 4.4 2.0 - - + +
99A ASN* 3.1 45.9 + - - +
100A MET 3.2 2.1 + - - +
102A PHE* 1.3 106.5 - + - +
104A LEU* 1.3 56.9 + - - +
105A LEU 3.2 0.4 - - - -
106A PRO* 3.5 22.0 - - + +
107A PRO* 2.9 27.1 - - + +
17C PRO 4.5 4.0 - - - +
18C LEU* 3.9 28.7 - - + -
21C ALA* 3.4 21.1 - - + +
22C LEU* 5.9 0.2 - - - +
101L TGL 4.3 19.1 - - + -
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Residues in contact with LEU 104 (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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100A MET* 3.1 34.9 + - + +
102A PHE 3.1 0.6 - - - -
103A TRP* 1.3 78.6 - - - +
105A LEU* 1.3 59.1 + - - +
107A PRO* 3.2 6.5 - - - +
108A SER* 3.1 28.2 + - - -
152A LEU* 4.1 20.5 - - + +
155A VAL* 3.9 16.8 - - + -
156A SER* 3.8 37.5 - - - +
159A LEU* 4.4 4.7 - - + -
607A PGV 4.4 10.3 - - + -
21C ALA* 4.0 11.4 - - + +
24C 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