Contacts of the strand formed by residues 41 - 50 (chain A) in PDB entry 2YD6
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLN* 3.3 18.6 - - + +
35A GLY* 5.4 0.9 - - - -
40A VAL* 1.3 75.2 - - - +
42A SER* 1.3 64.0 + - - +
43A PHE* 4.8 6.3 - - + -
82A LEU 3.8 0.7 - - - +
83A ARG* 3.4 2.3 - - - -
84A ILE* 2.9 35.3 + - + +
87A LEU* 3.8 14.3 - - + +
113A LEU* 3.7 32.1 - - + -
211A TYR* 4.5 0.9 - - - -
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Residues in contact with SER 42 (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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33A GLN* 2.7 31.4 + - - -
40A VAL* 4.1 5.2 - - - +
41A ALA* 1.3 75.5 + - - +
43A PHE* 1.3 62.0 + - - +
44A ILE* 5.2 2.6 - - - +
81A VAL* 4.0 12.2 - - - +
82A LEU 3.2 5.6 - - - -
83A ARG* 4.1 12.6 + - - +
160A PHE* 3.8 25.8 - - - -
163A PHE 4.9 0.5 + - - -
211A TYR* 2.7 27.1 + - - -
1222A CL 4.1 5.0 - - - +
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 4.0 4.9 - - + -
31A VAL 3.3 27.1 - - - -
33A GLN* 4.0 11.0 - - + -
41A ALA* 4.8 5.2 - - + -
42A SER* 1.3 77.7 - - - +
44A ILE* 1.3 61.9 + - - +
57A TRP* 3.6 23.4 - + + -
81A VAL* 3.2 6.4 - - - +
82A LEU* 2.9 51.3 + - + +
84A ILE* 4.7 6.5 - - + -
96A TYR* 4.6 9.6 - + - -
111A THR* 3.6 27.4 - - + -
112A ARG 3.7 20.4 - - - -
113A LEU* 3.8 37.0 - - + -
1222A CL 3.7 2.2 - - + -
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Residues in contact with ILE 44 (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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28A ARG* 3.6 55.6 - - - +
29A THR 3.4 3.3 - - - +
30A PRO* 3.1 25.6 - - - +
42A SER 5.2 1.8 - - - +
43A PHE* 1.3 79.5 - - - +
45A CYS* 1.3 67.6 + - - +
57A TRP* 4.3 0.7 - - - -
74A PHE* 4.2 25.1 - - + -
80A SER 3.7 2.0 - - - -
81A VAL* 4.1 12.6 - - + -
160A PHE* 4.3 16.6 - - + -
165A PRO* 3.9 22.7 - - + -
1222A CL 3.2 15.4 - - + +
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Residues in contact with CYS 45 (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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26A PHE* 3.5 22.2 - - - -
28A ARG 3.5 6.5 - - - -
30A PRO* 4.1 5.8 - - + -
44A ILE* 1.3 79.7 - - - +
46A GLN* 1.3 62.5 + - - +
55A ILE* 3.5 6.3 - - + +
57A TRP* 3.6 16.4 - - + -
74A PHE* 4.2 1.6 - - - -
79A GLY* 3.4 1.9 - - - -
80A SER 2.9 32.7 + - - +
98A CYS* 2.0 50.0 - - + -
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Residues in contact with GLN 46 (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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26A PHE* 3.4 6.6 - - - -
27A THR* 2.8 38.1 + - - +
28A ARG* 2.9 28.8 + - + +
45A CYS* 1.3 76.0 - - - +
47A ALA* 1.3 66.6 + - - +
55A ILE* 4.1 1.6 - - - -
74A PHE* 3.7 20.4 - - + -
75A ASP* 2.8 37.6 + - - +
78A SER 3.4 13.5 - - - -
79A GLY* 4.0 3.6 - - - -
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Residues in contact with ALA 47 (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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24A PRO* 4.7 0.7 - - + -
25A ARG 3.1 17.7 - - - +
26A PHE* 4.2 4.3 - - + -
27A THR* 4.0 5.6 - - - +
46A GLN* 1.3 79.2 - - - +
48A THR* 1.3 61.7 + - - +
53A PRO* 3.6 18.1 - - + +
55A ILE* 4.8 2.2 - - + -
75A ASP* 4.7 2.1 - - - +
78A SER* 2.9 32.1 - - - -
100A ALA* 3.7 24.7 - - + -
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Residues in contact with THR 48 (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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24A PRO* 3.3 5.0 - - - +
25A ARG* 2.9 77.2 + - + +
27A THR* 3.8 15.0 - - + +
47A ALA* 1.3 75.2 - - - +
49A GLY* 1.3 67.3 + - - +
52A ARG* 5.7 2.9 + - - -
53A PRO* 3.6 9.3 - - - +
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Residues in contact with GLY 49 (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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22A THR* 3.6 16.8 - - - -
23A PRO 4.0 5.2 - - - -
48A THR* 1.3 83.7 + - - +
50A ASP* 1.3 60.5 + - - +
51A PRO 3.2 17.7 - - - +
52A ARG* 3.6 11.6 + - - +
53A PRO* 3.6 3.1 - - - +
102A ASN* 4.3 2.5 - - - -
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Residues in contact with ASP 50 (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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21A GLU* 3.2 22.7 + - - +
22A THR* 2.8 49.3 + - + +
49A GLY* 1.3 73.3 - - - +
51A PRO* 1.3 71.7 + - - +
52A ARG 4.0 0.2 - - - +
102A ASN* 3.6 2.2 + - - -
104A VAL* 3.8 0.3 - - - +
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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