Contacts of the strand formed by residues 37 - 43 (chain A) in PDB entry 3HV3
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 SER 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASN* 4.5 13.8 + - - -
16A THR* 4.2 17.3 - - - +
18A TRP* 3.5 19.8 + - - -
31A GLY 3.5 11.7 - - - -
32A SER* 4.1 9.0 - - - +
36A GLY* 1.3 74.2 - - - -
38A VAL* 1.3 61.5 + - - +
53A LYS* 3.5 2.5 - - - +
54A LYS* 2.8 40.0 + - - +
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Residues in contact with VAL 38 (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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14A ASN* 4.8 1.2 + - - -
18A TRP* 4.1 0.9 - - - -
29A PRO* 3.4 5.0 - - - +
30A VAL* 2.8 50.5 + - + -
31A GLY 3.1 14.0 + - - +
32A SER 5.4 4.3 - - - -
36A GLY 5.3 1.3 - - - +
37A SER* 1.3 81.5 - - - +
39A CYS* 1.3 61.5 + - - +
51A ALA* 3.8 20.6 - - + -
52A VAL 3.2 11.2 - - - +
53A LYS* 4.0 20.6 - - + +
169A PHE* 5.9 0.7 - - + -
361A R49 3.8 32.5 - - + +
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Residues in contact with CYS 39 (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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13A LEU* 3.9 20.2 - - - -
14A ASN* 5.0 1.1 - - - -
18A TRP* 3.6 31.5 - - + -
27A LEU* 4.1 15.9 - - + -
28A SER 3.2 15.5 - - - +
29A PRO* 3.8 22.4 - - - -
38A VAL* 1.3 77.7 - - - +
40A ALA* 1.3 63.6 + - - +
41A ALA 3.9 0.2 + - - -
51A ALA* 3.4 1.8 - - - -
52A VAL* 2.7 39.3 + - + +
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Residues in contact with ALA 40 (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 ASN 3.4 2.8 - - - +
27A LEU* 3.2 5.2 - - - -
28A SER* 2.7 45.3 + - - +
30A VAL* 4.0 15.4 - - + +
39A CYS* 1.3 71.5 - - - +
41A ALA* 1.3 58.7 + - - +
49A ARG* 5.2 5.4 - - - +
50A VAL 3.3 6.7 - - - -
108A LEU* 3.9 30.3 - - + -
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Residues in contact with ALA 41 (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 TYR* 4.4 6.1 - - + -
25A GLN 3.5 6.1 - - - +
26A ASN* 4.2 2.7 - - - -
27A LEU* 3.6 27.4 - - + -
40A ALA* 1.3 77.4 - - - +
42A PHE* 1.3 60.4 + - - +
49A ARG* 3.4 10.4 - - - +
50A VAL* 2.8 48.0 + - + -
52A VAL* 4.3 9.0 - - + -
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Residues in contact with PHE 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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23A ARG 3.4 1.0 - - - +
24A TYR* 3.5 2.0 - - - -
25A GLN* 2.9 38.3 + - + +
26A ASN* 4.6 14.7 - - + +
41A ALA* 1.3 73.7 - - - +
43A ASP* 1.3 67.9 + - - +
44A THR* 3.1 31.2 + - + +
47A GLY* 2.9 36.8 - - - -
48A LEU 3.8 5.6 - - - -
49A ARG* 4.6 12.6 - - + -
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Residues in contact with ASP 43 (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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23A ARG* 2.8 51.2 + - - +
24A TYR* 3.7 12.6 - - + -
41A ALA 4.0 1.0 + - - -
42A PHE* 1.3 71.9 - - - +
44A THR* 1.3 57.4 + - - +
45A LYS* 3.0 11.3 + - - +
46A THR* 2.9 24.9 + - - +
47A GLY* 2.8 32.7 + - - -
48A LEU* 2.9 18.9 + - - +
50A VAL* 3.9 18.6 - - + +
87A LEU* 5.7 3.1 - - - +
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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