Contacts of the strand formed by residues 41 - 50 (chain B) in PDB entry 2YD7
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 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B GLN* 3.4 20.0 - - + +
35B GLY* 5.3 1.3 - - - -
40B VAL* 1.3 75.7 - - - +
42B SER* 1.3 62.9 + - - +
43B PHE* 4.9 5.2 - - + -
82B LEU 3.8 0.9 - - - +
83B ARG* 3.4 1.9 - - - -
84B ILE* 2.8 36.8 + - + +
87B LEU* 3.9 14.3 - - + +
113B LEU* 3.7 30.5 - - + -
211B TYR* 4.5 0.4 - - - -
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Residues in contact with SER 42 (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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33B GLN* 2.7 25.8 + - - +
41B ALA* 1.3 76.6 + - - +
43B PHE* 1.3 61.6 + - - +
44B ILE* 4.3 2.5 + - - +
81B VAL* 4.0 9.4 - - - +
82B LEU 3.1 8.3 - - - -
83B ARG* 4.0 18.0 + - - +
160B PHE* 3.9 26.1 - - - -
163B PHE 5.0 0.3 + - - -
211B TYR* 2.6 30.6 + - - -
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Residues in contact with PHE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO* 3.9 6.1 - - + -
31B VAL 3.2 28.3 - - - +
33B GLN* 3.7 26.7 - - + -
41B ALA* 4.9 1.8 - - + -
42B SER* 1.3 74.3 - - - +
44B ILE* 1.3 61.6 + - - +
57B TRP* 3.5 22.2 - - + -
81B VAL* 3.3 6.4 - - - +
82B LEU* 2.8 54.1 + - + +
84B ILE* 4.3 15.5 - - + -
96B TYR* 4.5 5.8 - + - -
111B THR* 3.4 29.2 - - + -
112B ARG 3.9 5.6 - - - -
113B LEU* 3.7 34.5 - - + -
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Residues in contact with ILE 44 (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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28B ARG* 3.7 43.7 - - + +
29B THR 3.5 3.3 - - - +
30B PRO* 3.0 31.3 - - + +
42B SER 5.1 2.0 - - - +
43B PHE* 1.3 76.5 - - - +
45B CYS* 1.3 64.4 + - - +
46B GLN* 5.5 0.2 - - + -
57B TRP* 4.1 0.4 - - - -
74B PHE* 4.1 22.4 - - + -
80B SER 3.7 3.6 - - - +
81B VAL* 4.0 14.1 - - + -
160B PHE* 4.3 15.9 - - + -
165B PRO* 3.6 31.2 - - + -
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Residues in contact with CYS 45 (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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26B PHE* 3.5 22.0 - - - -
28B ARG 3.4 6.7 - - - -
30B PRO* 4.0 6.1 - - + -
44B ILE* 1.3 79.2 - - - +
46B GLN* 1.3 64.3 + - - +
55B ILE* 4.3 4.8 - - + +
57B TRP* 3.6 17.9 - - + -
74B PHE* 4.4 0.5 - - - -
78B SER 4.2 0.3 - - - +
79B GLY* 3.4 1.9 - - - -
80B SER* 2.8 36.3 + - - +
98B CYS* 2.0 50.0 - - + -
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Residues in contact with GLN 46 (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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26B PHE* 3.4 7.1 - - - -
27B THR* 2.7 41.5 + - - +
28B ARG* 2.8 39.4 + - + +
45B CYS* 1.3 76.4 - - - +
47B ALA* 1.3 61.6 + - - +
55B ILE* 5.0 0.9 - - - -
74B PHE* 3.5 23.1 - - + -
75B ASP* 3.0 35.3 + - - +
78B SER 3.4 12.1 - - - +
79B GLY* 4.0 3.8 - - - -
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Residues in contact with ALA 47 (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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24B PRO* 4.7 0.2 - - + -
25B ARG 3.2 14.6 - - - +
26B PHE* 4.1 6.7 - - + -
27B THR* 4.0 4.9 - - - +
46B GLN* 1.3 78.7 - - - +
48B THR* 1.3 60.8 + - - +
53B PRO* 3.6 13.1 - - + +
55B ILE* 4.2 4.5 - - + +
75B ASP* 4.4 3.8 - - - +
78B SER* 3.0 30.3 + - - -
100B ALA* 3.7 30.5 - - + -
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Residues in contact with THR 48 (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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24B PRO* 3.1 5.5 - - - +
25B ARG* 2.7 72.5 + - + +
27B THR* 4.0 13.8 - - + +
47B ALA* 1.3 74.0 - - - +
49B GLY* 1.3 64.1 + - - +
53B PRO* 3.7 8.6 - - - +
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Residues in contact with GLY 49 (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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22B THR* 3.6 12.8 - - - -
23B PRO 3.8 10.5 - - - -
24B PRO* 4.3 2.5 - - - -
48B THR* 1.3 85.7 + - - +
50B ASP* 1.3 63.1 + - - +
51B PRO 3.2 15.9 - - - +
52B ARG* 3.5 8.8 + - - +
53B PRO* 3.9 2.6 - - - +
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Residues in contact with ASP 50 (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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21B GLU* 3.2 21.4 + - - +
22B THR* 2.8 49.5 + - + +
49B GLY* 1.3 76.2 - - - +
51B PRO* 1.4 69.8 + - - +
52B ARG 4.6 0.7 + - - -
102B ASN* 3.6 1.6 - - - -
104B VAL* 4.8 0.5 - - - +
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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