Contacts of the strand formed by residues 102 - 108 (chain B) in PDB entry 2DYY
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 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ILE 2.8 11.7 + - - +
74B LYS* 3.3 9.2 - - + +
75B VAL 2.9 24.9 + - - +
101B PRO* 1.3 72.7 - - - +
103B ARG* 1.3 59.8 + - - +
104B VAL* 5.6 0.2 - - - -
18C SER 3.6 11.7 - - - +
20C ALA* 4.2 1.6 - - - -
21C ILE* 2.9 11.5 - - + +
28C PHE* 3.5 27.6 - - + +
29C ILE 4.1 1.3 - - - -
30C ALA* 3.6 18.4 - - + +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.4 11.7 - - + +
77B VAL* 4.5 12.1 - - + -
101B PRO 3.6 0.6 + - - -
102B ALA* 1.3 75.0 - - - +
104B VAL* 1.3 72.7 + - - +
105B ALA* 3.5 24.5 - - - +
14C ILE* 4.5 8.1 + - - +
17C TYR* 3.0 64.0 + - + +
18C SER 4.3 1.4 + - - -
30C ALA* 3.4 9.3 - - - +
31C GLY* 2.7 28.8 + - - +
112C PRO* 5.6 3.6 - - - +
118C GLU* 4.7 0.5 - - - +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LYS* 4.5 8.7 - - + -
75B VAL 2.9 6.7 + - - +
76B THR* 3.3 21.4 - - + +
77B VAL 2.8 24.5 + - - -
103B ARG* 1.3 82.5 - - - +
105B ALA* 1.3 65.9 + - - +
106B VAL* 4.5 3.6 - - + -
29C ILE 4.9 0.4 - - - +
30C ALA* 4.5 3.1 - - - -
31C GLY 3.8 6.1 - - - +
78C TYR* 3.9 21.5 - - + +
118C GLU* 3.6 16.4 - - - +
120C GLU* 3.7 46.9 - - + +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 3.4 14.6 - - + +
79B LEU* 4.8 6.5 - - + -
103B ARG* 3.5 30.9 - - - +
104B VAL* 1.3 79.7 - - - +
106B VAL* 1.3 62.2 + - - +
112C PRO* 3.5 21.7 - - + +
118C GLU* 2.9 22.5 + - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B THR* 5.7 1.1 - - + -
77B VAL 2.9 8.1 + - - +
78B TYR* 3.3 28.1 - - + -
79B LEU* 3.0 28.9 + - - +
104B VAL* 4.5 1.8 - - + -
105B ALA* 1.3 84.0 - - - +
107B GLU* 1.3 63.0 + - - +
108B VAL* 4.2 10.1 - - + -
78C TYR* 3.7 42.2 - - + -
108C VAL* 4.4 4.3 - - + -
110C ARG 4.2 3.6 - - - -
111C LEU* 4.0 10.8 - - + -
112C PRO* 5.3 0.7 - - - -
118C GLU* 3.4 16.8 - - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 3.1 27.9 - - + +
80B LYS 4.6 2.7 - - - -
81B ASP* 2.8 32.1 - - - +
106B VAL* 1.3 78.5 - - - +
108B VAL* 1.3 61.7 + - - +
108C VAL* 3.0 26.7 - - - +
109C SER* 3.3 6.5 + - - -
110C ARG* 3.2 61.2 + - + +
111C LEU 6.2 0.4 - - - -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.4 28.0 - - + -
107A GLU 3.4 9.0 - - - +
108A VAL* 3.9 21.5 - - + +
78B TYR* 4.3 9.0 - - + -
79B LEU 2.8 16.4 + - - +
80B LYS* 4.0 1.1 - - - +
81B ASP* 3.4 23.0 + - - +
106B VAL* 4.2 11.9 - - + -
107B GLU* 1.3 80.8 - - - +
109B SER* 1.3 68.0 + - - +
110B ARG 4.2 2.2 - - - +
111B LEU* 3.4 19.5 - - + -
108C VAL* 4.1 11.4 - - + +
109C SER* 3.5 10.7 + - - +
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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